Nucleic acid encoding a cobalamin-dependent methionine synthase polypeptide

ABSTRACT

The present invention relates to nulceotide sequences encoding enzymatically active cobalamin-methionine synthase and functional fragments thereof being modified in comparison to the respective wild-type enzyme such that said enzymes show reduced product inhibition by methionine. The present invention also relates to polypeptides being encoded by such nucleotide sequences and host cells comprising such nucleotide sequences. Furthermore, the present invention relates to methods for producing methionine in host organisms by making use of such nucleotide sequences.

FIELD OF THE INVENTION

The present invention relates to nucleotide sequences encodingenzymatically active cobalamin-methionine synthase and functionalfragments thereof being modified in comparison to the respectivewild-type enzyme such that said enzymes show a reduced productinhibition by methionine. The present invention also relates topolypeptides being encoded by such nucleotide sequences and host cellscomprising such nucleotide sequences. Furthermore, the present inventionrelates to methods for producing methionine in host organisms by makinguse of such nucleotide and amino acid sequences.

TECHNOLOGICAL BACKGROUND

Currently, worldwide annual production of methionine is about 500,000tons. Methionine is the first limiting amino acid in livestock ofpoultry feed and due to this, mainly applied as feed supplement. Incontrast to other industrial amino acids, methionine is almostexclusively applied as a racemate produced by chemical synthesis. Sinceanimals can metabolise both stereoisomers of methionine, direct feed ofthe chemically produced racemic mixture is possible (D′Mello and Lewis,Effect of Nutrition Deficiencies in Animals: Amino Acids, Rechgigl(Ed.), CRC Handbook Series in Nutrition and Food, 441-490, 1978).

However, there is still a great interest in replacing the existingchemical production by a biotechnological process. This is due to thefact that at lower levels of supplementation L-methionine is a bettersource of sulfur amino acids than D-methionine (Katz et al., (1975)Poult. Sci., 545: 1667-74). Moreover, the chemical process uses ratherhazardous chemicals and produces substantial waste streams. All thesedisadvantages of chemical production could be avoided by an efficientbiotechnological process.

For other amino acids such as glutamate, fermentation production methodsare known. For these purposes, certain microorganisms such asEscherichia coli (E. coli) and Corynebacterium glutamicum (C.glutamicum) have proven to be particularly suited. The production ofamino acids by fermentation also has the particular advantage that onlyL-amino acids are produced. Further, environmentally problematicchemicals such as solvents, etc. which are used in chemical synthesisare avoided. However, fermentative production of methionine bymicroorganisms will only be an alternative to chemical synthesis if itallows for the production of methionine on a commercial scale at a pricecomparable to that of chemical production.

Hence, the production of L-methionine through large-scale culture ofbacteria developed to produce and secrete large quantities of thismolecule is a desirable goal. Improvements to the process can relate tofermentation parameters, such as stirring and supply of oxygen, or thecomposition of the nutrient media, such as the sugar concentrationduring fermentation, or the working up of the product by, for instance,ion exchange chromatography, or the intrinsic output properties of themicroorganism itself

Methods of mutagenesis and mutant selection are also used to improve theoutput properties of these methionine-producing microorganisms. Highproduction strains which are resistant to antimetabolites or which areauxotrophic for metabolites of regulatory importance are obtained inthis manner.

Recombinant DNA technology has also been employed for some years forimproving microorganism strains which produce L-amino acids byamplifying individual amino acid biosynthesis genes and investigatingthe effect on the amino acid production.

Rückert et al. (Journal of Biotechnology (2003), 104: 213-228) providean analysis of the L-methionine biosynthetic pathway in Corynebacteriumglutamicum. Known functions of MetZ (also known as MetY) and MetB couldbe confirmed and MetC (also known as AecD) was proven to be acystathionine-β-lyase. Further, MetE and MetH, which catalyse theconversion of L-homocysteine to L-methionine, were identified in thisstudy.

WO 02/097096 discloses nucleotide sequences from coryneform bacteriawhich code for the McbR repressor gene (also known as MetD) andprocesses for the preparation of amino acids using bacteria in whichthis McbR repressor gene is attenuated. According to WO 02/097096, theattenuation of the transcriptional regulator McbR improves theproduction of L-methionine in coryneform bacteria. It is furtherdescribed in WO 02/097096 that, in addition to the attenuation of theMcbR repressor gene, enhancing or overexpressing the MetB gene whichcodes for cystathionine-γ-synthase is preferred for the preparation ofL-methionine.

Selection of strains improved for the production of a particularmolecule is a time-consuming and difficult process. Therefore, there isstill a great need for microorganisms which efficiently produceL-methionine and/or have significantly increased contents ofL-methionine which can be utilized for obtaining methionine.

SUMMARY OF THE INVENTION

It is an object of the present invention to provide nucleotide sequenceswhich encode enzymatically active cobalamin-dependent methioninesynthases or functional fragments thereof having the property of reducedproduct inhibition by methionine.

Such nucleotide sequences encode preferably enzymatically activecobalamin-dependent methionine synthases or functional fragments thereofwhich carry at least one mutation in their amino acid sequence comparedto the respective wild-type amino acid sequence such that these enzymesshow reduced product inhibition by methionine, i.e. the enzymaticactivity is inhibited by methionine to a lesser extent than for thewild-type enzymes and polypeptides. Such nucleotide sequences may e.g.be DNA and/or RNA sequences with DNA sequences being preferred.

It is a further object of the present invention to provide polypeptidesand preferably proteins which are encoded by such nucleotide sequences.

Yet another object of the present invention is to provide vectors whichcomprise such nucleotide sequences and can be used for expression ofsuch nucleotide sequences and polypeptides in host cells.

Another object of the present invention relates to host cells whichexpress the aforementioned nucleotide and polypeptide sequences.

Yet another object of the present invention relates to the use of suchnucleotide and polypeptide sequences for producing methionine and/orincreasing the efficiency of methionine production in host organisms.

The present invention also relates to methods for producing methionineby expressing said nucleotide and polypeptide sequences in hostorganisms.

According to one embodiment of the invention, nucleotide and preferablyDNA sequences are provided which encode an enzymatically activecobalamin-dependent methionine synthase or functional fragments thereofhaving the property of reduced product inhibition by methionine. In oneembodiment such nucleotide and preferably DNA sequences encodeenzymatically active cobalamin-dependent methionine synthases orfunctional fragments thereof which carry at least one mutation in theiramino acid sequence compared to the respective wild-type amino acidsequences, such that the enzymatic activity of said enzymatically activecobalamin-dependent methionine synthases or of said functional fragmentsshows reduced product inhibition as a consequence of the at least onemutation. This means that the enzymatic activity of the mutated enzymesor functional fragments thereof is inhibited by methionine to a lesserextent compared to the respective wild-type sequences.

Such nucleotide and preferably DNA sequences may also allow theconstruction of host organisms which product and secrete preferablylarge quantities of the desired molecule, i.e. L-methionine.

In a further embodiment of the present invention, such nucleotide andpreferably DNA sequences encode enzymatically active cobalamin-dependentmethionine synthases or functional fragments thereof which carry atleast one mutation in SEQ ID NO. 1 such that the encoded polypeptidesshow reduced product inhibition by methionine compared to the respectivewild-type polypeptides.

Yet another embodiment of the present invention relates to nucleotideand preferably DNA sequences that encode enzymatically activecobalamin-dependent methionine synthases or functional fragments thereofwhich carry at least one mutation in their homocysteine-binding domainsuch that these polypeptides show reduced product inhibition bymethionine. A typical homocysteine-binding domain is that of MetH of C.glutamicum. The corresponding DNA sequence is SEQ ID No. 24 while theamino acid sequence is SEQ ID No. 2.

In yet another embodiment of the present invention, nucleotide andpreferably DNA sequences encode enzymatically active cobalamin-dependentmethione synthases or functional fragments thereof which carry at leastone mutation in SEQ ID Nos. 3 to 18 such that these polypeptides showreduced product inhibition by methionine.

One embodiment of the present invention relates to nucleotide andpreferably DNA sequences which encode enzymatically activecobalamin-dependent methionine synthases or functional fragments thereofwhich carry at least one mutation in a position corresponding to M33,F86 or S134 of the cobalamin-dependent methionine synthase MetH of C.glutamicum. The DNA sequence of MetH of C. glutamicum is that of SEQ IDNo. 23. The amino acid sequence of MetH of C. glutamicum is that of SEQID No. 1.

The present invention in one embodiment also relates to nucleotide andpreferably DNA sequences which encode polypeptides that are at least50%, at least 60%, at least 70%, at least 80%, at least 85%, at least90%, at least 95%, at least 96%, at least 97%, at least 98% or at least99% identical to the polypeptides being encoded by the afore-mentionednucleotide sequences which carry at least one mutation in thesesequences compared to the wild-type sequences such that the resultingenzymatically active cobalamin-dependent methionine synthases orfunctional fragments thereof show reduced product inhibition bymethionine.

Thus, the present invention on one embodiment relates to nucleotide andpreferably DNA sequences which encode polypeptides that are at least50%, at least 60%, at least 70%, at least 80%, at least 85%, at least90%, at least 95%, at least 96%, at least 97%, at least 98% or at least99% identical to the polypeptides being encoded by any of SEQ ID Nos.1to 18 with the proviso that these polypeptides carry at least onemutation in these sequences such that the resulting enzymatically activecobalamin-dependent methionine synthases or functional fragments thereofshow reduced product inhibition by methionine.

Yet another embodiment of the present invention relates to nucleotideand preferably DNA sequences that are at least 30%, at least 40%, atleast 50%, at least 60%, at least 70%, at least 80%, at least 85%, atleast 90%, at least 95%, at least 96%, at least 97%, at least 98% or atleast 99% identical to the aforementioned nucleotide and preferably DNAsequences.

Thus, in one embodiment the present invention relates to nucleotide andpreferably DNA sequences that are at least 30%, at least 40%, at least50%, at least 60%, at least 70%, at least 80%, at least 85%, at least90%, at least 95%, at least 96%, at least 97%, at least 98% or at least99% identical to e.g. SEQ ID No. 23 or SEQ ID No. 24 with the provisothat the nucleotide sequences carry additionally at least one mutationsuch that the resulting enzymatically active cobalamin-dependentmethionine synthases or functional fragments thereof show reducedproduct inhibition by methionine.

In preferred embodiments these nucleotide and preferably DNA sequencesare isolated or recombinant nucleotide and preferably DNA sequences.

Another embodiment of the present invention relates to nucleotide andpreferably DNA sequences that hybridise under stringent conditions tothe aforementioned nucleotide sequences.

Other embodiments of the present invention relate to nucleotide andpreferably DNA sequences encoding enzymatically activecobalamin-dependent methionine synthases or functional fragments thereofwhich carry at least one mutation with respect to the corresponding wildtype sequences, the enzymatic activity of which is at least 10%, 20%,30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% and preferably at least a factorof 2, 3, 4, 5, 10, 20, 50, 100, 200, 500 or 1000 less inhibited in thepresence of 20 mM methionine compared to respective wild-typecobalamin-dependent methionine synthases or functional fragmentsthereof.

The present invention also relates to vectors which comprise theaforementioned nucleotide and preferably DNA sequences in operativelinkage to promoter and termination sequences such that these nucleotidesequences can be expressed in host organisms.

Other embodiments of the present invention relate to polypeptides whichare encoded by the aforementioned nucleotide and preferably DNAsequences.

Yet another embodiment of the present invention relates to host cellswhich comprise the aforementioned nucleotide and preferably DNAsequences.

In one embodiment of the present invention, such host cells express theaforementioned nucleotide and preferably DNA sequences, preferably fromone of the aforementioned vectors.

According to a further embodiment of the present invention, such hostcells are selected from microorganisms and yeasts. In one embodiment,the microorganism is selected from the group consisting of e.g.coryneform bacteria, microbacteria, streptomycetaceae, salmonella,Escherichia coli, Shigella, Bacillus, Serratia, Pseudomonas, S. coel orThermotoga maritima.

While any host cell or host organism in accordance with the presentinvention must comprise the above mentioned nucleotide and preferablyDNA sequences which encode for enzymatically active cobalamin-dependentmethionine synthases or functional fragments thereof having reducedproduct inhibition by menthionine, one embodiment of the presentinvention relates to host cells in which additionally the endogenousgene(s) for cobalamin-dependent methionine synthase(s) is/are deleted orfunctionally disrupted.

Other embodiments of the invention relate to host cells and hostorganisms in which at least one of the nucleotide and preferably DNAsequences in accordance with the present invention is expressed and inwhich the amount and/or activity of at least one polypeptide beingencoded by the following nucleotide sequences is increased in comparisonto the corresponding initial host organism:

-   -   nucleotide sequence coding for aspartate kinase lysC,    -   nucleotide sequence coding for glycerine aldehyde-3-phosphate        dehydrogenase gap,    -   nucleotide sequence coding for 3-phosphoglycerate kinase pgk,    -   nucleotide sequence coding for pyruvatecarboxylase pyc,    -   nucleotide sequence coding for triosephosphate isomerase tpi,    -   nucleotide sequence coding for homoserin-O-acetyltransferase        metA,    -   nucleotide sequence coding for cystathione-gamma-synthase metB,    -   nucleotide sequence coding for cystathione-gamma-lyase metC,    -   nucleotide sequence coding for serine-hydroxymethyl transferase        glyA,    -   nucleotide sequence coding for O-acetylhomoserine-sulfhydrylase        metY,    -   nucleotide sequence coding for phosphoserine aminotransferase        serC,    -   nucleotide sequence coding for phosphoserine-phosphatase serB,    -   nucleotide sequence coding for serine acetyltransferase cysE,    -   nucleotide sequence coding for homoserine-dehydrogenase hom,    -   nucleotide sequence coding for methionine synthase metE,    -   nucleotide sequence coding for        phosphoadenosine-phosphosulfate-reductase cysH,    -   nucleotide sequence coding for sulfate adenylyl        transferase-subunit I,    -   nucleotide sequence coding for CysN-sulfate adenylyl        transferase-subunit 2,    -   nucleotide sequence coding for ferredoxine-NADP-reductase,    -   nucleotide sequence coding for ferredoxine,    -   nucleotide sequence coding for        glucose-6-phosphate-dehydrogenase, and/or    -   nucleotide sequence coding for fructose-1-6-bisphosphatase.

Another embodiment of the present invention relates to host cells andhost organisms in which one of the nucleotide and preferably DNAsequences in accordance with the present invention is expressed and inwhich additionally the amount and/or activity of at least onepolypeptide being encoded by the following nucleotide sequences isdecreased with respect to the corresponding initial organism:

-   -   nucleotide sequence coding for homoserine kinase thrB,    -   nucleotide sequence coding for threonine dehydratase ilvA,    -   nucleotide sequence coding for threonine synthase thrC,    -   nucleotide sequence coding for        meso-diaminopimelate-D-dehydrogenase ddh,    -   nucleotide sequence coding for phosphoenolpyruvate carboxy        kinase pck,    -   nucleotide sequence coding for glucose-6-phosphate-6-isomerase        pgi,    -   nucleotide sequence coding for pyruvate-oxidase poxB,    -   nucleotide sequence coding for dihydrodipicolinate synthase        dapA,    -   nucleotide sequence coding fro dihydrodipicolinate reductase        dapB,    -   nucleotide sequence coding for diaminopicolinate-decarboxylase        lysA,    -   nucleotide sequence coding for glycosyl transferase and/or    -   nucleotide sequence coding for lactate hydrogenase.

Another aspect of the invention relates to host cells and organisms inwhich the efficiency and/or yield and/or amount of methionine productionis increased by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%,100% and preferably at least by a factor of 2, 3, 4, 5, 10, 20, 50, 100or 1000 in comparison to a host cell or host organism in which nonucleotide sequence in accordance with the invention is expressed.

Other embodiments of the present invention relate to methods forproducing methionine in a host cell or organism wherein a nucleotide andpreferably DNA or polypeptide sequence in accordance with the inventionis expressed in the host cell.

Other embodiments of the present invention relate to methods forproducing methionine wherein one of the aforementioned host cells isused.

One aspect of the present invention relates to a method for producingmethionine in which one of the aforementioned host cells is cultivatedand methionine is subsequently isolated. The present invention alsorelates to the use of the aforementioned host cells for producingmethionine and to the use of nucleotide and preferably DNA sequences inaccordance with the present invention to produce methionine and hostcells which are useful in producing methionine.

DESCRIPTION OF THE DRAWINGS

FIG. 1 is a model of the pathway for L-methionine biosynthesis inmicroorganisms such as C. glutamicum. Enzymes involved are MetA(homoserine transacetylase), MetB (cystathione-gamma-synthase), MetZ(O-acetylhomoserine sulfhydrolase), MetC (cystathione-beta-lyase),cob(I)alamin-dependent methionine synthase I (MetH) andcob(I)alamin-independent methionine synthase II (MetE).

FIG. 2 shows a sequence alignment of the cob(I)alamin-dependentmethionine synthases of C. glutamicum, S. coel, E. coli and Thermotogamaritima.

FIG. 3 depicts the amino acid sequence (SEQ ID No. 1, a)) and DNAsequence (SEQ ID No. 23), b)) of cob(I)alamin-dependent methioninesynthase MetH of C. glutamicum.

FIG. 4 depicts the amino acid sequence (SEQ ID No. 2, b)) and DNAsequence (SEQ ID No. 24, b)) of the homocysteine binding domain ofcob(I)alamin-dependent methionine synthase MetH of C. glutamicumcomprising amino acids 1 to 244.

FIG. 5 depicts amino acid sequences (SEQ ID Nos. 3 to 18) of conservedregions within the homocysteine binding domain of cob(I)alamin-dependentmethionine synthases of C. glutamicum, S. coel, E. coli and Thermotogamaritima.

FIG. 6 depicts the amino acid sequence (SEQ ID No. 19, a)) and DNAsequence (SEQ ID No. 25, b)) of the cob(I)alamin-dependent methioninesynthase MetH of C. glutamicum carrying a M33A mutation.

FIG. 7 depicts the amino acid sequence (SEQ ID No. 20, a)) and DNAsequence (SEQ ID No. 26, b)) of the cob(I)alamin-dependent methioninesynthase MetH of C. glutamicum carrying a M33L mutation.

FIG. 8 depicts the amino acid sequence (SEQ ID No. 21, a)) and DNAsequence (SEQ ID No. 27, b)) of the cob(I)alamin-dependent methioninesynthase MetH of C. glutamicum carrying a F86L mutation.

FIG. 9 depicts the amino acid sequence (SEQ ID No. 22, a)) and DNAsequence (SEQ ID No. 28, b)) of the cob(I)alamin-dependent methioninesynthase MetH of C. glutamicum carrying a 5134N mutation.

DETAILED DESCRIPTION OF EXEMPLARY EMBODIMENTS

Before describing in detail exemplary embodiments of the presentinvention, the following definitions are given.

The terms “nucleotide sequences in accordance with the presentinvention” and “DNA sequences in accordance with the present invention”refer to the corresponding sequences as mentioned above that encodepolypeptides being enzymatically active cobalamin-dependent methioninesynthases or functional fragments thereof that show a reduced productinhibition by methionine. The term “reduced product inhibition bymethionine” will be defined further below. The term “polypeptide” meansto encompass proteins and typically relates to polypeptides with morethan 20 amino acids.

The term “efficiency of methionine synthesis” describes the carbon yieldof methionine. This efficiency is calculated as a percentage of theenergy input which enters the system in the form of a carbon substrate.Throughout the invention this value is given in percent values ((molmethionine) (mol carbon substrate)⁻¹·100), unless indicated otherwise.Preferred carbon sources according to the present invention are sugars,such as mono-, di-, or polysaccharides. For example, sugars selectedfrom the group consisting of glucose, fructose, manose, galactose,libose, sorbose, lactose, maltose, sucrose, raffinose, starch orcellulose may serve as particularly preferred carbon sources.

The term “increased efficiency of methionine synthesis” relates to thecomparison between an organism being a host cell that has beengenetically modified to express nucleotide and preferably DNA sequencesin accordance with the present invention and which has a higherefficiency of methionine synthesis compared to the initial organismwhich does not express the nucleotide and preferably the DNA sequencesin accordance with the present invention.

The initial organism which does not express nucleotide and preferablyDNA sequences in accordance with the present invention may be awild-type organism. Alternatively, it may be an organism that hasalready been optimised for methionine production and thus over-expressescertain genes of the methionine synthesis pathway. Alternatively, aninitial organism which has already been optimised for methionineproduction may show a reduced expression for certain enzymes of themethionine pathway.

The terms “methionine pathway” and “methionine biosynthesis pathway” areart-recognised and describe a series of reactions which take place in awild-type organism and lead to the biosynthesis of L-methionine. Thesepathways may vary from organism to organism. The details of anorganism-specific pathway can be taken from textbooks and the scientificliterature on the internet websitehttp://www.genome.jp/kegg/metabolism.html. In particular, a methioninepathway within the meaning of the present invention is shown in FIG. 1.

The term “yield of methionine” describes the yield of methionine whichis calculated as the amount of methionine obtained per weight cell mass.

The terms “organism”, “host organism”, “host cell” or “microorganism”for the purposes of the present invention refer to any organism that iscommonly used for the production of amino acids such as methionine. Inparticular, these terms relate to procaryots, lower eucaryots and fungi.A preferred group of the above-mentioned organisms comprises actinobacteria, cyano bacteria, proteo bacteria, Chloroflexus aurantiacus,Pirellula sp. 1, halo bacteria and/or methanococci, preferablycoryneform bacteria, myco bacteria, streptomyces, salmonella,Escherichia coli, Shigella, Pseudomonas, S. coel or Thermotoga maritima.

Particularly preferred microorganisms are selected from Corynebacteriumglutamicum, Escherichia coli, microorganisms of the genus Bacillus,particularly Bacillus subtilis, microorganisms of the genusStreptomyces, or of the genus Thermotoga, particularly Thermotogamaritima.

The organisms of the present invention may, however, also compriseyeasts such as Schizosaccharomyces pombe or S. cerevisiae and Pichiapastoris.

The terms “L-methionine over-producing organism”, “methionineover-producing organism” or “methionine-producing organism” for thepurposes of the present invention refer to an “organism”, “hostorganism” or “microorganism” in which compared to an initial organismwhich does not express nucleotide and preferably DNA sequences inaccordance with the present invention, the efficiency and/or yieldand/or amount of methionine production is increased at least by 10%,20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% or at least by a factor of2, 3, 4, 5, 10, 15, 20, 50, 100, 500 and 1000 or more.

The term “metabolite” refers to chemical compounds that are used in themetabolic pathways of organisms as precursors, intermediates and/or endproducts. Such metabolites may not only serve as chemical buildingunits, but may also exert a regulatory activity on enzymes and theircatalytic activity. It is known from the literature that suchmetabolites may inhibit or stimulate the activity of enzymes (Stryer,Biochemistry, (1995) W.H. Freeman & Company, New York, New York).

For the purposes of the present invention, the term “externalmetabolite” comprises substrates such as glucose, sulfate, thiosulfate,sulfite, sulfide, ammonia, oxygen etc.

If, in the context of the present invention, reference is made to thecontent of a nucleotide sequence or the content of a polypeptide encodedby the nucleotide sequence, this refers to the amount of nucleic acidand polypeptide being encoded by such nucleic sequences as they can bedetermined for the respective host organism comprising such nucleotidesequences or polypeptides.

If reference is made to the activity of a nucleotide sequence thistypically, for the purposes of the present invention, means to encompassthe activity of the polypeptide or protein that is encoded by such anucleotide sequence.

If, in the context of the present invention, it is stated that theamount of nucleotide sequence is increased with respect to a wild-typeor initial organism, this means that the amount of this nucleotidesequence and the amount of the polypeptide that is encoded by thenucleic acid are increased in comparison to an organism which is notgenetically manipulated with respect to this specific nucleotidesequence or polypeptide. This may be achieved by introducing acorresponding exogenous nucleotide sequence into a host organism and thecomparison then refers to the host organism expressing the nucleotidesequence and the initial organism into which the nucleotide sequence hasnot been introduced. Alternatively, the amount of nucleotide sequencemay be increased by manipulating other regulatory sequences or theendogenous sequences within an organism.

Thus, increasing the amount of a nucleotide sequence may be achieved byintroducing exogenous sequences or manipulating endogenous sequencesthat are responsible for the level of expression of the respectivenucleotide sequences.

If, in the context of the present invention, it is stated that theactivity of a nucleotide sequence is increased with respect to aninitial organism, this refers to a situation where typically theactivity of the polypeptide that is encoded by this nucleotide sequenceis increased in comparison to the initial organism. Increasing theactivity may be achieved by increasing the amount of the nucleotidesequence, and/or by introducing mutations in nucleotide sequencesencoding polypeptides with increased activity.

Thus, increasing the activity of a nucleotide sequence and thepolypeptide being encoded thereby may be achieved by either introducingexogenous nucleotide sequences and/or introducing mutations into theregulatory and coding sequences of endogenous sequences that areresponsible for expressing the sequence of interest.

If, in the context of the present invention, it is stated that thecontent (amount) and/or activity of a nucleotide sequence, andconsequently of the polypeptide being encoded thereby, is decreased incomparison to an initial organism, the above definitions are to beapplied mutatis mutandis.

The terms “express,” “expressing,” “expressed” and “expression” refer toexpression of a gene product (e.g., a biosynthetic enzyme of a gene of apathway or reaction defined and described in this application) or anucleotide sequence. The expression can be done by genetic alteration ofthe e.g. microorganism that is used as an initial starting organism. Insome embodiments, a microorganism can be genetically altered (e.g.,genetically engineered) to express a gene product such as a polypeptideat an increased level relative to that produced by the initialmicroorganism or in a comparable microorganism which has not beenaltered. Genetic alteration includes, but is not limited to, altering ormodifying regulatory sequences or sites associated with expression of aparticular gene (e.g. by adding strong promoters, inducible promoters ormultiple promoters or by removing regulatory sequences such thatexpression is constitutive), modifying the chromosomal location of aparticular gene, altering nucleic acid sequences adjacent to aparticular gene such as a ribosome binding site or transcriptionterminator, increasing the copy number of a particular gene, modifyingproteins (e.g., regulatory proteins, suppressors, enhancers,transcriptional activators and the like) involved in transcription of aparticular gene and/or translation of a particular gene product, or anyother conventional means of deregulating expression of a particular geneusing routine in the art (including but not limited to use of antisensenucleic acid molecules, for example, to block expression of repressorproteins).

The terms “overexpress”, “overexpressing”, “overexpressed” and“overexpression” refer to expression of a gene product (e.g. amethionine biosynthetic enzyme or a gene or a pathway or a reactiondefined and described in this application) or a nucleotide sequence at alevel greater than that present prior to a genetic alteration of theinitial microorganism. In some embodiments, a microorganism can begenetically altered (e.g., genetically engineered) to express a geneproduct or nucleotide sequence at an increased level relative to thatproduced by the initial microorganism. Genetic alteration includes, butis not limited to, altering or modifying regulatory sequences or sitesassociated with expression of a particular gene (e.g., by adding strongpromoters, inducible promoters or multiple promoters or by removingregulatory sequences such that expression is constitutive), modifyingthe chromosomal location of a particular gene, altering nucleic acidsequences adjacent to a particular gene such as a ribosome binding siteor transcription terminator, increasing the copy number of a particulargene, modifying proteins (e.g., regulatory proteins, suppressors,enhancers, transcriptional activators and the like) involved intranscription of a particular gene and/or translation of a particulargene product, or any other conventional means of deregulating expressionof a particular gene using routine in the art (including but not limitedto use of antisense nucleic acid molecules, for example, to blockexpression of repressor proteins). Examples for the overexpression ofgenes in organisms such as C. glutamicum can be found in Eikmanns et al(Gene. (1991) 102, 93-8).

In some embodiments, a microorganism can be physically orenvironmentally altered to express a gene product or nucleotide sequenceat an increased or lower level relative to level of expression of thegene product or nucleotide sequence by the initial microorganism. Forexample, a microorganism can be treated with or cultured in the presenceof an agent known or suspected to increase transcription of a particularnucleotide sequence and/or translation of a particular nucleotidesequence such that transcription and/or translation are enhanced orincreased. Alternatively, a microorganism can be cultured at atemperature selected to increase transcription of a particularnucleotide sequence or gene and/or translation of a particularnucleotide sequence or gene product such that transcription and/ortranslation are enhanced or increased.

The terms “disrupt”, “disrupted”, “disruption”, “deregulate,”“deregulated” and “deregulation” refer to alteration or modification ofat least one gene or nucleotide sequence in e.g. a microorganism,wherein the alteration or modification results in increasing efficiencyor yield of methionine production in the microorganism relative tomethionine production in absence of the alteration or modification. Insome embodiments, a gene or nucleotide sequence that is altered ormodified encodes an enzyme in a biosynthetic pathway, such that thelevel or activity of the biosynthetic enzyme in the microorganism isaltered or modified. In some embodiments, at least one gene that encodesan enzyme in a biosynthetic pathway is altered or modified such that thelevel or activity of the enzyme is enhanced or increased relative to thelevel in presence of the unaltered or wild type gene. In someembodiments, the biosynthetic pathway is the methionine biosyntheticpathway. Deregulation also includes altering the coding region of one ormore genes to yield, for example, an enzyme that is feedback resistantor has a higher or lower specific activity. Also, deregulation furtherencompasses genetic alteration of genes encoding transcriptional factors(e.g., activators, repressors) which regulate expression of genes in themethionine and/or cysteine biosynthetic pathway.

The phrase “deregulated pathway or reaction” refers to a biosyntheticpathway or reaction in which at least one gene that encodes an enzyme ina biosynthetic pathway or reaction is altered or modified such that thelevel or activity of at least one biosynthetic enzyme is altered ormodified. The phrase “deregulated pathway” includes a biosyntheticpathway in which more than one gene has been altered or modified,thereby altering level and/or activity of the corresponding geneproducts/enzymes. In some cases the ability to “deregulate” a pathway(e.g., to simultaneously deregulate more than one gene in a givenbiosynthetic pathway) in a microorganism arises from the particularphenomenon of microorganisms in which more than one enzyme (e.g., two orthree biosynthetic enzymes) are encoded by genes occurring adjacent toone another on a contiguous piece of genetic material termed an“operon.” In other cases, in order to deregulate a pathway, a number ofgenes must be deregulated in a series of sequential engineering steps.

The term “operon” refers to a coordinated unit of genetic material thatcontains a promoter and possibly a regulatory element associated withone or more, preferably at least two, structural genes (e.g., genesencoding enzymes, for example, biosynthetic enzymes). Expression of thestructural genes can be coordinately regulated, for example, byregulatory proteins binding to the regulatory element or byanti-termination of transcription. The structural genes can betranscribed to give a single mRNA that encodes all of the structuralproteins. Due to the coordinated regulation of genes included in anoperon, alteration or modification of the single promoter and/orregulatory element can result in alteration or modification of each geneproduct encoded by the operon. Alteration or modification of aregulatory element includes, but is not limited to, removing endogenouspromoter and/or regulatory element(s), adding strong promoters,inducible promoters or multiple promoters or removing regulatorysequences such that expression of gene products is modified, modifyingthe chromosomal location of the operon, altering nucleic acid sequencesadjacent to the operon or within the operon such as a ribosome bindingsite, codon usage, increasing copy number of the operon, modifyingproteins (e.g., regulatory proteins, suppressors, enhancers,transcriptional activators and the like) involved in transcription ofthe operon and/or translation of the gene products of the operon, or anyother conventional means of deregulating expression of genes routine inthe art (including, but not limited to, use of antisense nucleic acidmolecules, for example, to block expression of repressor proteins).

In some embodiments, recombinant microorganisms described herein havebeen genetically engineered to overexpress a bacterially derived gene orgene product. The terms “bacterially-derived” and “derived-frombacteria” refer to a gene which is naturally found in bacteria or a geneproduct which is encoded by a bacterial gene.

Amino acids comprise the basic structural units of all proteins, and assuch are essential for normal cellular functioning in organisms. Theterm “amino acid” is well known in the art. The proteinogenic aminoacids, of which there are 20 species, serve as structural units forproteins, in which they are linked by peptide bonds, while thenon-proteinogenic amino acids are not normally found in proteins (seeUllmann's Encyclopaedia of Industrial Chemistry, Vol. A2, pages 57-97,VCH, Weinheim (1985)). Amino acids may be in the D- or L-opticalconfiguration, although L-amino acids are generally the only type foundin naturally-occurring proteins. Biosynthetic and degradative pathwaysof each of the 20 proteinogenic amino acids have been well characterizedin both prokaryotic and eukaryotic cells (see, for example, Stryer, L.Biochemistry, 3rd edition, pages 578-590 (1988)).

The essential amino acids, i.e. histidine, isoleucine, leucine, lysine,methionine, phenylalanine, threonine, tryptophan and valine, which aregenerally a nutritional requirement due to the complexity of theirbiosynthesis, are readily converted by simple biosynthetic pathways tothe remaining 11 non-essential amino acids, i.e. alanine, arginine,asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline,serine and tyrosine.

Higher animals retain the ability to synthesize some of these aminoacids, but the essential amino acids must be supplied from the diet inorder for normal protein synthesis to occur. Apart from their functionin protein biosynthesis, these amino acids are interesting chemicals intheir own right, and many have been found to have various applicationsin the food, feed, chemical, cosmetic, agricultural and pharmaceuticalindustries.

Lysine is an important amino acid in the nutrition not only of humans,but also of monogastric animals, such as poultry and swine. Glutamate ismost commonly used as a flavour additive, and is widely used throughoutthe food industry as are aspartate, phenylalanine, glycine and cysteine.Glycine, L-methionine and tryptophan are all utilized in thepharmaceutical industry. Glutamine, valine, leucine, isoleucine,histidine, arginine, proline, serine and alanine are of use in both thepharmaceutical and cosmetic industries. Threonine, tryptophan andD/L-methionine are common feed additives (Leuchtenberger, W. (1996),Amino acids—technical production and use, p.466-502 in Rehm et al.(editors) Biotechnology, Vol. 6, Chapter 14a, VCH: Weinheim).Additionally, these amino acids have been found to be useful asprecursors for the synthetic of synthetic amino acids and proteins suchas N-acetyl cysteine, S-carboxymethyl-L-cysteine,(S)-5-hydroxytryptophan and others described in Ullmann's Encyclopaediaof Industrial Chemistry, Vol. A2, p.57-97, VCH: Weinheim, 1985.

The biosynthesis of these natural amino acids in organisms capable ofproducing them, such as bacteria, has been well characterized (forreview of bacterial amino acid biosynthesis and regulation therefor (seeUmbarger H. E. (1978), Ann. Rev. Biochem. 47:533-606). Glutamate issynthesized by the reductive amination of α-ketoglutarate, anintermediate in the citric acid cycle. Glutamine, proline and arginineare each subsequently produced from glutamate. The biosynthesis ofserine is a three-step process beginning with 3-phosphoglycerate (anintermediate in glycolysis), and resulting in this amino acid afteroxidation, transamination, and hydrolysis steps. Both cysteine andglycine are produced from serine; the former by the condensation ofhomocysteine with serine, and the latter by transferral of theside-chain β-carbon atom to tetrahydrofolate, in a reaction catalysed byserine transhydroxymethylase. Phenylalanine and tyrosine are synthesizedfrom the glycolytic and pentose phosphate pathway precursorserythrose-4-phosphate and phosphoenolpyruvate in a nine-stepbiosynthetic pathway that differ only at the final two steps after thesynthesis of prephenate. Tryptophan is also produced from these twoinitial molecules, but its synthesis is an eleven-step pathway. Tyrosinemay also be synthesized from phenylalanine in a reaction catalysed byphenylalanine hydroxylase. Alanine, valine and leucine are allbiosynthetic products of pyruvate, the final product of glycolysis.Aspartate is formed from oxaloacetate, an intermediate of the citricacid cycle. Asparagine, methionine, threonine and lysine are eachproduced by the conversion of aspartate. Isoleucine may be formed fromthreonine. A complex nine-step pathway results in the production ofhistidine from 5-phosphoribosyl-1-pyrophosphate, an activated sugar.

Amino acids in excess of the protein synthesis needs of the cell cannotbe stored and are instead degraded to provide intermediates for themajor metabolic pathways of the cell (for review see Stryer, L.,Biochemistry, 3rd edition, Chapter 21 “Amino acid degradation and theurea cycle”, p. 495-516 (1988)). Although the cell is able to convertunwanted amino acids into useful metabolic intermediates, amino acidproduction is costly in terms of energy, precursor molecules, and theenzymes necessary to synthesise them.

Amino acid biosynthesis can be regulated by feedback inhibition, inwhich the presence of a particular amino acid serves to slow or entirelystop its own production (for overview of feedback mechanisms in aminoacid biosynthetic pathways, see Stryer, L., Biochemistry, 3rd edition,Chapter 24: “Biosynthesis of amino acids and heme”, p.575-600 (1988)).If this feedback inhibition is mediated by an amino acid forming theproduct of the regulated reaction or pathway, one typically speaks of“product inhibition”. Thus, the output of any particular amino acid islimited by the amount of that amino acid present in the cell.

The Gram-positive soil bacterium Corynebacterium glutamicum is widelyused for the industrial production of different amino acids. Whereas thebiosynthesis of lysine and glutamate, the main industrial products, hasbeen studied for many years, knowledge about the regulation of themethionine biosynthetic pathway is limited.

However, at least the key enzymes of the pathway are known (see FIG. 1).C. glutamicum activates homoserine by acetylation withhomoserine-O-acetyltransferase (MetA) (EC 2.3.1.31). It was furthershown that both transsulfuration and direct sulfhydrylation are used toproduce homocysteine (Hwang et al. (2002), J. Bacteriol., 1845:1277-86). Transsulfuration is catalyzed by cystathionine-γ-synthase(MetB) (EC 2.5.1.48) (Hwang et al. (1999) Mol Cells, 93:

300-8). In this reaction, cysteine and O-acetyl-homoserine are combinedto cystathionine, which is hydrolyzed by the cystathionine-β-lyase (MetCwhich is also known as AecD) (EC 4.4.1.8) (Kim et al. (2001), Mol. Cell,112:220-5, Ruckert et al. (2003), vide supra) convertsO-acetylhomoserine and sulfide into homocysteine and acetate. Finally,C. glutamicum has two different enzymes for the S-methylation ofhomocysteine yielding methionine (Lee et al. (2003), Appl. Microbiol.Biotechnol. 625-6, 459,67; Ruckert et al. (2003), vide supra), i.e. acob(I)alamin dependent methionine synthase I (MetH) (EC 2.1.1.13) and acob(I)alamin independent methionine synthase II (MetE) (EC 2.1.1.14).The former utilizes 5-methyltetrahydrofolate and the latter5-methyltetrahydropteroyltri-L-glutamate as the methyl donor.

Recently, a putative transcriptional regulator protein of theTetR-family was found (Rey et al. (2003), Journal of Biotechnology, 103:51-65). This regulator was shown to repress the transcription of severalgenes belonging to methionine and sulfur metabolism. The gene knockoutof the regulator protein led to an increased expression of hom encodinghomoserine dehydrogenase, metZ encoding O-acetylhomoserinesulfhydrolase, metK encoding S-adenosylmethionine (SAM) synthase (EC2.5.1.6), cysK encoding cysteine synthase (EC 2.5.1.47), cysl encoding aputative NADPH dependant sulfite reductase, and finally ssuD encoding anputative alkanesulfonate monooxygenase. Rey et al. (MolecularMicrobiology 2005, 56, 871-887) also found that the metB gene issignificantly induced in a mcbR minus strain.

As regards the cob(I)alamin-dependent methionine synthases which, forthe purposes of the present invention, are also designated ascobalamin-dependent methionine synthases or MetH, it has been shown thatactivity of this enzyme is inhibited by its product, i.e. methionine(Banerjee et al. (1990), Biochemistry, 29:11101-1109).

This so-called “product inhibition” of methionine probably accounts forthe high need of methionine production which has been calculated torequire an energy input of 7 mol ATP and 8 mol NADPH per moleculemethionine (Neidhardt et al. (1990) Physiology of the Bacterial Cell: AMolecular Approach, Sunderland, Mass., USA, Sinauer Associates, Inc.).Thus, methionine is the one amino acid with respect to which a cell hasto provide the most energy.

As a consequence thereof, methionine-producing organisms have evolvedmetabolic pathways that are under strict control with respect to therate and amount of methionine synthesis (Neidhardt (1996) E. coli and S.typhimurium, ASM Press Washington). These regulation mechanisms includee.g. feedback control mechanisms such as the above-mentioned productinhibition of the activity of the cobalamin-dependent methioninesynthase.

The product inhibition of the cobalamin-dependent methionine synthasecreates a particular bottleneck when producing methionine over-producingmicroorganisms, as this enzyme catalyses the last step in the methioninebiosynthesis pathway. Thus, microorganisms which have been optimizedwith respect to expression of other enzymes involved in the methioninebiosynthesis pathway may ultimately prove to be unusable for efficientmethionine production, because even though e.g. elevated amounts ofhomocysteine have accumulated in these microorganisms, homocysteinecannot be efficiently methylated to methionine, as the cells will shutoff this enzymatic step once enough methionine has been produced.

As can be taken from FIG. 1, the methylation of homocysteine tomethionine is catalysed by two types of enzymes. Thecobalamin-independent methionine synthase, which is also designated asMetE in view of its low turnover numbers has a rather limited catalyticcapability (Gonzales et al. (1992) Journal of Biology 31:6045-6056).Cobalamin-dependent synthase, however, seems to be a rather goodcandidate for this approach given its turnover number of about 1500min⁻¹ (Gonzales et al. (1992) vide supra).

One of the objectives of the present invention is to resolve thelimitations for the non-chemical methionine production in organisms.This and other objectives which will be become apparent from the ensuingdescription are solved by the independent claims. Preferred embodimentsare described in the dependent claims.

The core of the present invention lies at the surprising finding that itis possible to produce mutants of cobalamin-dependent methioninesynthases in which the inhibition of the enzymatic activity by theproduct methionine is significantly reduced.

These mutants, which show reduced product inhibition, thus continue toefficiently catalyze the methylation of homocysteine into methionine ina cobalamin-dependent manner, even when methionine levels are reachedfor which a microorganism will usually down-regulate the enzymaticactivity of this last step. As these mutants decouple the enzymaticactivity of cobalamin-dependent methionine synthase from the feedbackcontrol mechanism of product inhibition, they allow the construction ofhost organisms that produce methionine continuously and efficiently.

While such enzymatically active cobalamin-dependent methionine synthasemutants have been specifically isolated for the MetH enzyme of C.glutamicum, it is justified to assume that corresponding mutants existfor cobalamin-dependent methionine synthases in other organisms such asE.coli, S. coel and T. maritima. This is supported by the fact thatcobalamin-dependent methionine synthases from E.coli, S. coel, C.glutamicum, Thermotoga maritima show a high degree of sequencesimilarity particularly in the homocysteine-binding domain which is theregion that has been identified by the present invention to be mostsuitable for introducing mutations that reduce the product inhibition ofcobalamin-dependent methionine synthases in C. glutamicum.

Before specific and preferred cobalamin-dependent methionine synthasemutants are described in more detail, an overview is given for theproperties of cobalamin-dependent methionine synthases in general.

Cobalamin-dependent methionine synthase catalyses the transfer of amethyl group from methyltetrahydrofolate to homocysteine generatingtetrahydrofolate and methionine (Banerjee (1990) vide supra). The MetHgene from E.coli as well as from other organisms including T. maritima,S. coel and C. glutamicum have been cloned, and in some casescharacterized (Banerjee (1990) vide supra; Ludwig et al. (1997) Annu.Rev. Biochem., 66:269-313; Yamada et al. (1999) Journal of BiologicalChemistry, 274:33571-33576; Evans et al. (2004) Proc. Natl. Acad. Sci.USA, 101:3729-3736).

The enzyme contains a non-covalently bound cobalamin prosthetic groupthat functions as an intermediary in the methyl-transferase reaction.During catalysis, the enzyme shuttles between the E-methyl cobalamin andE-cob(I)alamin states, being alternately demethylated by homocysteineand remethylated by methyltetrahydrofolate.

An assay to measure the activity of methionine synthase is described inthe literature (Drummond et al. (1995) Analytical Biochemistry,228:323-329). This latter reference is specifically incorporated byreference, as far as it describes assays for the characterization ofcobalamin-dependent methionine synthases. Thus, the passages starting onpage 324, right column (“Materials and Methods”) to page 326, leftcolumn (“Results”) of the Drummond et al. reference form part of thedisclosure of this application as far as non-radioactive assays forcharacterization of cobalamin-dependent methionine synthases areconcerned. The assay described by Drummond et al. can be used fordetermining the influence of the product methionine on the enzymaticactivity of cobalamin-dependent methionine synthases along the samelines as described by the aforementioned reference of Banerjee et al.(1990) vide supra for radioactive assays on page 11102, left column(“Experimental procedures”) to page 11103, left column (“Results”) andpage 11103, right column (“Product inhibition data”) to page 11104, leftcolumn (“Pre-steady-state kinetic analysis of catalysis”) and Table IIof the Banerjee et al. reference. As can be taken from the latterreference cobalamin-dependent methionine synthases are inhibited bymethionine in a non-competitive manner.

The cobalamin-dependent methionine synthase of E.coli which isrepresentative for other cobalamin-dependent methionine synthases fromorganisms such as C. glutamicum, etc. is a modular protein consisting ofvarious domains.

The first 352 residues of the E. coli enzyme comprise a homocysteinebinding region. Residues 353 to 649 are involved in the binding ofmethyltetrahydrofolate, while residues 650 to 896 bind the cobalaminco-factor. The carboxy terminal residues 897 to 1227 are required forreactivation of oxidized cob(II)alamin and bind adenosylsylmethyl. A 71kDa fragment, which comprises residues 2 to 649, contains thehomocysteine and methyltetrahydrofolate binding domains and catalysesmethyl transfer to and from exogenous cobalamin. The 98 kDa fragmentcomprises both the aforementioned substrate binding regions and thecobalamin binding domain and is capable of enzymatic turnover usingendogenous cobalamin co-factor.

The present invention at its core relates to enzymatically activecobalamin-dependent methionine synthases or functional fragments thereofwith reduced product inhibition by methionine.

As set out above, the present invention in one embodiment relates toenzymatically active cobalamin-dependent methionine synthases orfunctional fragments thereof which carry at least one mutation incomparison to the respective wild-type sequence with the mutation havingthe consequence that the mutated enzymatically activecobalamin-dependent methionine synthases or fragments thereof showreduced product inhibition by methionine.

The term “functional fragment” refers to fragments of wild-typefull-length versions of enzymatically active cobalamin-dependentmethionine synthases which are able to catalyse the methylation ofhomocysteine to methionine in a cobalamin-dependent manner and whichadditionally carry at least one mutation in their amino acid sequencewhich effects reduced product inhibition by methionine.

Cobalamin-dependent methionine synthases or functional fragments thereofin accordance with the invention are thus preferably considered to showreduced impaired product inhibition if the non-competitive inhibition ofthe methylation of homocysteine with methyltetrahydrofolate by theenzyme is influenced to a lesser extent by methionine than for therespective wild-type cobalamin-dependent methionine synthases orfunctional fragments thereof.

According to the present invention, an enzymatically activecobalamin-dependent methionine synthases or a functional fragmentsthereof are particularly considered to show reduced product inhibitionby methionine if, as a consequence of the mutation in the amino acidsequence, the inhibition of the activity by methionine, and preferablyby approximately 20 mM methionine is reduced by at least 10%, 20%, 30%,40%, 50%, 60%, 70%, 80%, 90%, 100% and preferably by at least a factorof 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 50, 100, 200, 500, 1000 or morecompared to the enzymatic activity of the respective wild type enzyme orfunctional fragment.

If the enzymatic activity of a wild-type cobalamin-dependent methioninesynthase or a functional fragment thereof is defined as 100%,cobalamin-dependent methionine synthases or functional fragments thereofwith reduced product inhibition by methionine in accordance with theinvention show an increased activity in the presence of methionine, andpreferably of approximately 20 mM methionine of at least 10%, 20%, 30%,40%, 50%, 60%, 70%, 80%, 90%, 100% and preferably by at least a factorof 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 50, 100, 200, 500, 1000 or morecompared to the enzymatic activity of the respective wild type enzyme orfunctional fragment.

The influence of methionine, and preferably of approximately 20 mMmethionine on the activity of either wild-type enzymatically activecobalamin-dependent methionine synthases or functional fragments thereofand enzymatically active cobalamin-dependent methionine synthases inaccordance with the present invention which have reduced productinhibition can be determined by the assay as described by Drummond etal. (vide supra).

By way of example, the cobalamin-dependent methionine synthase may beMetH of C. glutamicum and have an amino acid sequence of SEQ ID NO. 1.If a MetH version of SEQ ID NO. 1 which additionally carries at leastone mutation shows a reduced influence of methionine, and preferably ofapproximately 20 mM methionine on the activity of this enzyme under theabove test conditions, it will be considered as a cobalamin-dependentmethionine synthase with reduced product inhibition in accordance withthe present invention. The same would apply for a functional fragment ofMetH.

Accordingly, cobalamin-dependent methionine synthases of other organismssuch as E.coli, T. maritima, B. subtilis, S. coel which show asignificant homology to the wild-type MetH enzyme of C. glutamicum andwhich additionally carry mutations that reduce the product inhibition ofthese enzymes in comparison to their respective wild-type enzymes underthe above test conditions, will also be considered ascobalamin-dependent methionine synthases with a reduced productinhibition in accordance with the present invention.

According to the present invention, a significant sequence homologybetween two nucleic acid molecules or two polypeptides is generallyunderstood to indicate that the nucleotide sequences or the amino acidsequences, respectively, of a e.g. DNA molecules or proteins are atleast 30%, at least 40%, preferably at least 50%, at least 60%, at least70%, also preferably at least 80%, particularly preferably at least 90%,at least 95%, at least 96%, at least 97%, at least 98% and mostpreferably at least 99% identical. Additionally, the term “significantsequence homology” can require that the e.g. 90% identical nucleotidesequences encode polypeptides with the same function, e.g. acobalamin-dependent methionine synthase or functional fragment thereof.

Identity of two nucleotides sequences or polypeptides is understood tobe the identity of the nucleotides or amino acids over the respectiveentire length of the nucleotide sequences or the polypeptidesrespectively. Identity and Homology can be calculated using the lasergene software from DNA Star, Inc., Madison, Wis. (USA) applying theCLUSTAL method (Higgens et al. (1989), Comput. Appl. Biochi., 5(2):151).Homologies and identities for amino acid and nucleic acid sequences mayalso be calculated using algorithms which are based on algorithms byNiedelmann and Wunsch or Smith and Waterman. Software that may be usedfor these purposes are the programs Pil Aupa (J. Mol. Evolution (1987),25, 351-360; Higgins et al. (1989) Cabgos, 5:151) or the programs Gapand Bestfit (Niedelmann and Wunsch (1970), J. Mol. Biol., 48, 443-453and Smith and Waterman (1981) Adv. Appl. Math., 2, 482-489). For thepurposes of determining the identity of two sequences, the defaultparameters of the above software programs are used.

An example of determining a significant sequence homolgy betweencobalamin-dependent methionine synthases of different organisms isprovided by the sequence alignment of FIG. 2.

In one embodiment of the present invention, the mutations that lead toreduced product inhibition of the enzymatically activecobalamin-dependent methionine synthases or functional fragments thereofare located in the homocysteine binding region of the proteins. For theE.coli cobalamin-dependent methionine synthase, this region has beenmapped to amino acids 1 to 251.

It is well within the general knowledge of the person skilled in the artto identify corresponding domains in proteins that are related to theE.coli enzyme. In FIG. 2, a sequence alignment is shown for thecobalamin-dependent methionine synthases with wild-type sequences for C.glutamicum, E.coli, S. coel and T. maritima. From a comparison, it canbe seen that amino acids 1 to 251 of the E.coli enzyme correspond toamino acids 1 to 244 of the C. glutamicum enzyme, amino acids 1 to 212of the T. maritima enzyme and amino acids 1 to 243 of the S. coelenzyme.

Accordingly, one embodiment of the present invention relates tocobalamin-dependent methionine synthases which carry mutations in asequence that is significantly homologous to SEQ ID NO. 1 and whichprovide reduced product inhibition. In other embodiments of the presentinvention, the cobalamin-dependent methionine synthases with reducedproduct inhibition in accordance with the present invention have atleast one mutation in at least one of the following sequences:

SEQ ID No 3: X₁X₂X₃X₄X₅X₆X₇LX₈X₉X₁₀ wherein X₁ = S, V, R; X₂ =S, E, R; X₃ = E, A, Q; X₄ = F, L, V; X₅ = L, R, S; X₆ = D, E, A, K; X₇ =A, Q, L; X₈ = A, N, S; X₉ = N, T, E; X₁₀ = H, R SEQ ID No 4:X₁X₂X₃X₄DGX₅X₆GTX₇X₈X₉X₁₀X₁₁ wherein X₁ = V, I; X₂ = V, L; X₃ =I, V, L; X₄ = g, A, L; X₅ = A, G; X₆ = M, Y; X₇ = Q, M, E; X₈ =L, I, F; X₉ = Q, M; X₁₀ = G, A, S, K; X₁₁ = F, Q, Y SEQ ID No 5:X₁X₂X₃X₄X₅X₆X₇X₈X₉X₁₀X₁₁X₁₂X₁₃X₁₄X₁₅ wherein X₁ = L, P, Y; X₂ =D, T, N; X₃ = V, L, D, E; X₄ = E, D, A, L; X₅ = K, D, P; X₆ = Fexcept in T. marina, C. glutamicum, S. coel.; X₇ =R except in T. marina, C. glutamicum, S. coel.; X₈ =G except in T. marina, C. glutamicum, S. coel.; X₉ = Eexcept in T. marina, C. glutamicum, S. coel.; X₁₀ =R except in T. marina, C. glutamicum, S. coel.; X₁₁ =F except in T. marina, C. glutamicum, S. coel.; X₁₂ = Aexcept in T. marina, C. glutamicum, S. coel.; X₁₃ =D except in T. marina, C. glutamicum, S. coel.; X₁₄ =D, W except in T. marina; X₁₅ = F, P except in T. marina SEQ ID No 6:LX₁X₂X₃X₄PX₅X₆X₇X₈X₉X₁₀HX₁₁X₁₂YX₁₃ wherein X₁ = N, V; X₂ = D, L, I; X₃ =T, S, K; X₄ = R, K, A; X₅ = D, E; X₆ = V, I; X₇ = L, V, I; X₈ =R, A, L; X₉ = Q, S, A, K; X₁₀ = I, V; X₁₁ = R, E, N; X₁₂ =A, E, S; X₁₃ = F, I; SEQ ID No 7: X₁X₂GX₃DX₄X₅X₆TNTFX₇X₈X₉ wherein X₁ =E, A; X₂ = A, S; X₃ = A, V, S; X₄ = L, C, I, V; X₅ = V, I; X₆ =E, L; X₇ = G, N; X₈ = C, A, S; X₉ = N, T; SEQ ID No 8:X₁X₂X₃X₄X₅X₅X₆X₇X₈X₉ wherein X₁ = L, H, T, R; X₂ = P, S, I, M; X₃ =N, A, K; X₄ = L. M; X₅ = A, G, R; X₆ = D, E, K; X₇ = Y, H; X₈ =D, Q, G; X₉ = I, M, L; SEQ ID No 9:X₁X₂X₃X₄X₅X₆X₇X₈X₉X₁₀X₁₁X₁₂X₁₃X₁₄ARX₁₅X₁₆AX₁₇EX₁₈ wherein X₁ =A, P, E; X₂ = D, E, S; X₃ = R, L, K; X₄ = C, V, S, L; X₅ =R, H, A, D; X₆ = E, P; X₇ = L, I; X₈ = A, S, N, V; X₉ =Y, E, f, R; X₁₀ = K, A, N; X₁₁ = G, A; X₁₂ = T, A, V; X₁₃ =A, R, K; X₁₄ = V, L, I; X₁₅ = E, A, R; X₁₆ = V, C, A; X₁₇ = D, E; X₁₈ =F, M, W, K SEQ ID No 10: X₁X₂X₃X₄X₅X₆RX₇ wherein X₁ =G except in T. marina, A, R except in T. marina; X₂ =R, T except in T. marina; X₃ = N, D, P except in T. marina; X₄ =G, G, E except in T. marina; X₅ = M, R, K except in T. marina; X₆ =R, Q, P except in T. marina; X₇ = F, W, Y except in T. marina;SEQ ID No 11: VX₁GX₂X₃GPX₄X₅X₆X₇X₈X₉ wherein X₁ = V, L, A, F; X₂ =S, V, D; X₃ = L, M, I; X₄ = G, T; X₅ = T, N, G; X₆ = K, R, E; X₇ =L, T; X₈ = P, A; X₉ = S, T, Y; SEQ ID NO 12:X₁X₂X₃X₄X₅X₆X₇X₈X₉X₁₀X₁₁X₁₂X₁₃X₁₄X₁₅X₁₆X₁₇X₁₈GX₁₉ wherein X₁ =F, Y; X₂ = >, T, D, E; X₃ = D, V, G, E; X₄ = L, F; X₅ = R, V, Y; X₆ =G, D, A, E; X₇ = H, A, N; X₈ = Y, E; X₉ = K, Q, R; X₁₀ = E, R; X₁₁ =A, N, S, T; X₁₂ = A, T, V; X₁₃ = L, E, K; X₁₄ = G, A, I; X₁₅ =I, L, M; X₁₆ = I, V; X₁₇ = E, A, E; X₁₈ = G, E; X₁₉ = G, A, VSEQ ID No 13: DX₁X₂X₃X₄ET wherein X₁ = A, L, G; X₂ = F, L, I; X₃ =L, I; X₄ = I, V, F SEQ ID NO 14: X₁DX₂LX₃X₄KAX₅VX₆X₇X₈X₉ wherein X₁ =Q, F, S; X₂ = L, T, I; X₃ = Q, N, E; X₄ = V, T, A, L; X₅ = A, S; X₆ =H, L, F; X₇ = G, A; X₈ = V, A; X₉ = Q, R, K SEQ ID No 15:X₁X₂X₃X₄X₅X₆X₇X₈X₉X₁₀X₁₁T wherein X₁ = L, V; X₂ = D, G, S; X₃ =T, L, V, R; X₄ = F, D, E; X₅ = L, V; X₆ = P, F; X₇ = I, L; X₈ =I, M; X₉ = C, V, I, A; X₁₀ = H, S; X₁₁ = V, G, M SEQ ID No 16:X₁X₂X₃X₄X₅X₆X₇X8LX₉GX₁₀X₁₁ wherein X₁ = V, I, F; X₂ = E, T, D; X₃ =T, D, E; X₄ = T, A, K; X₅ = G, S; X₆ = G except inT. marina, C. glutamicum, S. coel.; X₇ = T, R; X₈ = M, T, S; X₉ =M, L, S, T; X₁₀ = S, Q, T; X₁₁ = E, T, D SEQ ID No 17: X₁X₂X₃X₄X₅X₆X₇wherein X₁ = G, E, A; X₂ = A, N; X₃ = A, F; X₄ = L, Y, A; X₅ =T, N, I; X₆ = A, S, T; X₇ = L, F SEQ ID No 18:X₁X₂X₃X₄X₅X₆X₇GX₈NCX₉X10GPX₁₁E wherein X₁ = P, H, E; X₂ = L, A; X₃ =G, E, D; X₄ = I, A; X₅ = D, L; X₆ = M, T, A; X₇ = I, F, L; X₈ =L, I; X₉ = A, S; X₁₀ = T, L; X₁₁ = D, A, E

In the context of the present invention the term “mutation” as regardsan amino acid sequence relates to an amino acid substitution, insertionor deletion in the wild type sequence of cobalamin-dependent methioninesynthases or functional fragments thereof with the requirement that themutation changes the enzymatic activity such that the resultingpolypeptide is still capable of catalyzing transfer of a methyl groupfrom methyltetrahydrofolate to homocysteine in a cobalamin-dependentmanner, with the mutated enzyme or functional fragment thereof havingreduced product inhibition by methionine as defined above.

The person skilled in the art will be able to introduce mutations e.g.in the aforementioned amino acid sequences SEQ ID Nos. 1 to 18 and, e.g.relying on the assay described above, will be able to determine whetherthe resulting polypeptides are enzymatically active and show reducedproduct inhibition in the presence by methionine.

For such mutations, the person skilled in the art will consider inparticular non-conservative amino acid substitutions, meaning that thewild-type amino acid is replaced with an amino acid of differentphysical-chemical properties. For example, if the wild-type sequencecomprises a charged amino acid such as aspartate, a non-conservativesubstitution will include a substitution of the aspartate for apositively charged amino acid such as lysine. Alternatively, anegatively charged amino acid such as aspartic acid or glutamic acid maybe replaced by a neutral amino acid such as glutamine, arginine ormethionine. The person skilled in the art will, of course, also considerconservative amino acid substitutions , i.e. replacement by amino acidswith comparable physico-chemical properties. An example is a replacementof Valine by Leucine.

An enzymatically active cobalamin-dependent methionine synthase orfunctional fragment thereof which carries a mutation in comparison tothe respective wild type sequences is not considered to be polypeptidein accordance with the invention if it does not show a reduced productinhibition by methionine as it can be determined by the above mentionedtest. Mutated polypeptides are also not considered to form part of theinvention if they are not enzymatically active. This also applies forthe nucleotide sequence encoding such polypeptides.

The nomenclature used throughout this specification for amino acids isthe common one letter code.

As regards SEQ ID NOS. 3 to 18, “mutation” in the case of amino acidsubstitution means that the amino acid of a specified position can bereplaced with any amino acid which is not specified for this particularposition. For example, for SEQ ID NO. 3, X₁ is specified to be S, V orR. A mutation may therefore comprise any amino acid substitution whichis not S, V, R. Similarly, residue X₄ of SEQ ID NO. 4, which is G, A, L,may be replaced by any amino acid which is not G, A, L.

The person skilled in the art is well aware that for any type of aminoacid substitution, deletion or insertion, it will be necessary todetermine whether the resulting polypeptide is (i) enzymatically activeand (ii) shows a reduced product inhibition of the enzymatic activity inthe presence of methionine.

The above explanations of the term “mutation” as given for amino acidsequences correspondingly apply for nucleotide and preferably DNAsequences encoding such polypeptides.

Specific embodiments of the present invention in case of thecobalamin-dependent methionine synthase MetH of C. glutamicum includemutations in positions 33, 86 and 134, wherein the wild-type sequenceresidues are methionine, phenylanaline and serine, respectively.

In the case of position 33, the methionine may be changed to glycine oralanine. In case of the phenylalanine 86 position, phenylalanine may bechanged into leucine. In case of the serine residue at position 134, theresidue may be changed into asparagine. The corresponding amino acidsequences are depicted in SEQ ID Nos. 19 to 22 respectively, while thecorresponding DNA sequences are depicted in SEQ ID Nos. 25 to 28.

The person skilled in the art will realise that corresponding mutationsmay be introduced in e.g. the methionine residue 34 of the S. coelenzyme, the methionine residue 22 of the E.coli enzymeand the tyrosineresidue in position 22 of the Thermotoga enzyme. As regards thephenylalanine 86 position of the C. glutamicum enzyme, correspondingmutations in the E.coli system would be located at the phenyl alanineresidue 91, in the S. coel enzyme at the phenylalanine residue 86 and inthe Thermotoga maritimum enzyme at the phenylalanine residue 76.

As regards the serine 134 residue in the C. glutamicum enzyme,corresponding mutations in the S. coel enzyme would be located at serine134, in the E.coli enzyme at the valine residue 131 and in theThermotoga enzyme at the aspartate residue 124.

In these cases, the corresponding residues may be mutated into glycineand alanine for the methione/tyrosine residues, into leucine for thephenylalanine residue and into asparagine for the serine, valine oraspartate residue.

Correspondingly, instead of amino acid substitution, cobalamin-dependentmethionine synthases with reduced product inhibition in accordance withthe present invention may have deletions at the aforementionedpositions, or additional insertions.

Other embodiments of the present invention are nucleotide sequences andparticularly DNA sequences which encode the aforementioned polypeptidesand proteins. Some embodiments of the present invention relate to suchDNA sequences in an isolated form.

Other embodiments of the present invention relate to vectors whichcomprise in 5′-3′ direction:

-   -   a) a promoter sequence being functional for expression of        nucleotide sequences in a host cell    -   b) operatively linked thereto a nucleotide and preferably a DNA        sequence in accordance with the present invention, and    -   c) operatively linked thereto a termination sequence.

According to the present invention, operative linkage of a promoter, anucleotide sequence in accordance with the present invention and atermination sequence means that nucleotide sequences in accordance withthe present invention can be expressed in a host cell such that the hostcell expresses an enzymatically active cobalamin-dependent methioninesynthase or a functional fragment thereof that shows the reduced productinhibition by methionine as defined above.

In a preferred embodiment, these vectors comprise certain promoters andoptionally enhancer elements to allow for over-expression of e.g. DNAsequences encoding the aforementioned polypeptides and proteins.Specific embodiments for expression and over-expression of DNA sequencesare explained below.

Accordingly, another embodiment of the present invention relates to hostcells which comprise nucleotide and preferably DNA sequences or vectors,as have been described above.

By genetically amending organisms in accordance with the presentinvention, the efficiency and/or yield and/or amount of methioninesynthesis may be increased such that these methionine-overproducingorganisms are characterized in that methionine is produced with anincreased efficiency and/or increased yield and/or increased amount ofpreferably at least 10%, at least 20%, at least 30%, at least 40%, atleast 50%, at least 60%, at least 65%, at least 70%, at least 75%, atleast 80%, at least 90% or at least 100% compared to an initial organismthat does not express the nucleotide sequences in accordance with thepresent invention.

Compared to such an initial host organism, the efficiency and/or yieldand/or amount of methionine production in the methionine-producing hostorganism according to the present invention can increased preferably byat least by a factor of 2, 3, 4, 5, 6, 7, 8, 9, 10, 30, 50, 70, 100,200, 500 or at least by a factor of 1000.

The host organism according to the present invention may be selectedfrom the group consisting of coryneform bacteria, mycobacteria,streptomycetes, Salmonella, Escherichia coli, Shigella, Bacillus,Serratia, Pseudomonas, S. coel or T. maritima.

The organisms of the present invention may preferably comprise amicroorganism of the genus Corynebacterium, particularly Corynebacteriumacetoacidophilum, C. acetoglutamicum, C. acetophilum,C. ammoniagenes, C.glutamicum, C. lilium, C. nitrilophilus or C. spec.

The organisms in accordance with the present invention also comprisemembers of the genus Brevibacterium, such as Brevibacteriumharmoniagenes, Brevibacterium botanicum, B. divaraticum, B. flavam, B.healil, B. ketoglutamicum, B. ketosoreductum, B. lactofermentum, B.linens, B. paraphinolyticum and B. spec.

The organisms in accordance with the present invention also comprise S.coel.

The organisms in accordance with the present invention also comprisemembers of the genus Thermotoga, such as T. maritime.

In particular, Corynebacterium microorganisms may be selected from thegroup consisting of Corynebacterium glutamicum (ATCC 13032),Corynebacterium acetoglutamicum (ATCC 15806), Corynebacteriumacetoacidophilum (ATCC 13870), Corynebacterium thermoaminogenes (FERMBP-1539), Corynebacterium melassecola (ATCC 17965), Corynebacteriumglutamicum (KFCC10065), Corynebacterium glutamicum (DSM 17322),Corynebacterium efficiens (YS-3 4) and Corynebacterium glutamicum(ATCC21608).

Particularly preferred is the strain Corynebacterium glutamicumATCC13032 and all its derivatives. The strains ATCC 13286, ATCC 13287,ATCC 21086, ATCC 21127, ATCC 21128, ATCC 21129, ATCC 21253, ATCC 21299,ATCC 21300, ATCC 21474, ATCC 21475, ATCC 21488, ATCC 21492, ATCC 21513,ATCC 21514,

ATCC 21515, ATCC 21516, ATCC 21517, ATCC 21518, ATCC 21528, ATCC 21543,ATCC 21544, ATCC 21649, ATCC 21650, ATCC 21792, ATCC 21793, ATCC 21798,ATCC 21799, ATCC 21800, ATCC 21801, ATCC 700239, ATCC 21529, ATCC 21527,ATCC 31269 and ATCC 21526 which are known to produce lysine can alsopreferably be used. The other aforementioned strains can also be used.

The abbreviation KFCC means Korean Federation of Culture Collection,while the abbreviation ATCC means the American Type Strain CultureCollection Collection. The abbreviation DSM means the German ResourceCentre for Biological Material.

Microorganisms of the genus Escherichia may be selected from the groupcomprising Escherichia coli. Microorganisms of the genus Salmonella maybe selected from the group comprising Salmonella typhimurium.

Such host organisms may be engineered by introducing exogenousnucleotide sequences in accordance with the present invention, e.g. inthe form of vectors.

In addition, or alternatively, mutations such as those described abovewhich effect a reduced product inhibition may be introduced into theendogenous coding sequences for cobalamin-dependent methioninesynthases.

A further embodiment of the present invention relates to host cells inwhich nucleotide and preferably DNA sequences in accordance with thepresent invention which encode for enzymatically activecobalamin-dependent methionine synthases or functional fragments thereofhaving a reduced product inhibition in the presence of methionine areexpressed and in which additionally the endogenous gene(s) forcobalamin-dependent methionine synthase(s) is/are deleted orfunctionally disrupted.

The term “deleted” or “functional disruption” are, for the purposes ofthe present invention, equivalent to the statement that the contentand/or activity of the cobalamin-dependent methionine synthases as theyare encoded by the endogenous genes of the host organism are reduced.

How a reduction of the content and/or the activity and correspondingly adeletion and/or functional disruption of these endogenous genes forcobalamin-dependent methionine synthases may be achieved is describedbelow.

Other embodiments of the present invention relate to host cells in whichDNA sequences in accordance with the present invention, i.e. encodingcobalamin-dependent methionine synthases or fragments thereof with areduced product inhibition in the presence of methionine are expressedand in which the content and/or activity of at least one of thefollowing nucleotide sequences of group I is increased in comparison tothe respective initial organism:

-   -   nucleotide sequence coding for aspartate kinase lysC (EP 1 108        790 A2;    -   DNA SEQ ID No. 281),    -   nucleotide sequence coding for aspartate semialdehyde        dehydrogenase asd (EP 1 108 790 A2; DNA SEQ ID No. 282),    -   nucleotide sequence coding for glycerine aldehyde-3-phosphat        dehydrogenase gap (Eikmanns (1992), Journal of Bacteriology,        174: 6076-6086),    -   nucleotide sequence coding for 3-phosphoglycerate kinase pgk        (Eikmanns (1992), Journal of Bacteriology, 174: 6076-6086),    -   nucleotide sequence coding for pyruvate carboxylase pyc        (Eikmanns (1992), Journal of Bacteriology, 174: 6076-6086),    -   nucleotide sequence coding for triosephosphate isomerase tpi        (Eikmanns (1992), Journal of Bacteriology, 174: 6076-6086),    -   nucleotide sequence coding for homoserine-O-acetyl transferase        metA (EP 1 108 790; DNA SEQ ID No. 725),    -   nucleotide sequence coding for cystahionine gamma synthase metB        (EP 1 108 790; DNA SEQ ID No. 3491),    -   nucleotide sequence coding for cystahionine gamma lyase metC (EP        1 108 790; DNA SEQ ID No. 3061),    -   nucleotide sequence coding for serine hydroxymethyl transferase        glyA (EP 1 108 790; DNA SEQ ID No. 1110),    -   nucleotide sequence coding for O-acetylhomoserine sulfhydrylase        metY (EP 1 108 790; DNA SEQ ID No. 726),    -   nucleotide sequence coding for methylenetetrahydrofolate        reductase metF (EP 1 108 790; DNA SEQ ID No. 2379),    -   nucleotide sequence coding for phosphoserine amino transferase        serC (EP 1 108 790; DNA SEQ ID No. 928),    -   nucleotide sequence coding for phosphoserine phosphatase serB        (EP 1 108 790; DNA SEQ ID No. 334, DNA SEQ ID No. 467, DNA SEQ        ID No. 2767),    -   nucleotide sequence coding for serine acetyl transferase cysE        (EP 1 108 790; DNA SEQ ID No. 2818),    -   nucleotide sequence coding for homoserine dehydrogenase hom (EP        1 108 790; DNA SEQ ID No. 1306),    -   nucleotide sequence coding for methionine synthase metE (gene        bank accession number NCgl1094),    -   nucleotide sequence coding for cysteine synthase (gene bank        accession number NP_(—)601760, NP_(—)601337, NCgl2473,        NCgl2055),    -   nucleotide sequence coding for sulfite reductase (gene bank        accession numbers NP_(—)602008, NCgl2718)    -   nucleotide sequence coding for phosphoadenosine phosphosulfate        reductase (gene bank accession number NP_(—)602007, NCgl2717),    -   nucleotide sequence coding for sulfate adenylyl transferase        subunit 1 (gene bank accession number NP_(—)602005, NCgl2715),    -   nucleotide sequence coding for CysN-sulfate adenylyl transferase        subunit 2 (gene bank accession number NP_(—)602006, NCgl2716),    -   nucleotide sequence coding for ferredoxin NADP reductase (gene        bank accession number NP_(—)602009, NCgl2719),    -   nucleotide sequence coding for ferredoxine (gene bank accession        number NP_(—)602010, NCgl2720),    -   nucleotide sequence coding for glucose-6-phosphate dehydrogenase        (gene bank accession number NP_(—)600790, NCgl1514), and/or    -   nucleotide sequence coding for fructose-1-6-bisphosphatase (gene        bank accession number NP_(—)601294, NCgl2014).

Of course, such host organisms may show an increased content and/oractivity of nucleotide sequences which show a significant homology asdefined above for any of the aforementioned nucleotide sequences. Again,the term “significant sequence homology” requires that these nucleotidesequences encode polypeptides that have the respective enzymaticacitivity.

In other embodiments of the present invention, the host organism maycomprise nucleotide and preferably DNA sequences in accordance with theinvention which encode cobalamin-dependent methionine synthases oractive fragments thereof with reduced product inhibition in the presenceof methionine and additionally provides a reduced content and/oractivity of at least one of the following nucleotide sequences of groupII:

-   -   nucleotide sequence coding for homoserine kinase thrB (EP 1 108        790; DNA SEQ ID No. 3453),    -   nucleotide sequence coding for threonine dehydratase ilvA (EP 1        108 790; DNA SEQ ID No. 2328),    -   nucleotide sequence coding for threonin synthase thrC (EP 108        790; DNA SEQ ID No. 3486),    -   nucleotide sequence coding for meso        diaminopimelat-D-dehydrogenase ddh (EP 1 108 790; DNA SEQ ID No.        3494),    -   nucleotide sequence coding for phosphoenol pyruvate        carboxykinase pck (EP 1 108 790; DNA SEQ ID No. 3157),    -   nucleotide sequence coding for glucose-6-phosphatr-6-isomerase        pgi (EP 1 108 790; DNA SEQ ID No. 950),    -   nucleotide sequence coding for pyruvate oxidase poxB (EP 1 108        790; DNA SEQ ID No. 2873),    -   nucleotide sequence coding for dihydrodipicolinate synthase dapA        (EP 1 108 790; DNA SEQ ID No. 3476),    -   nucleotide sequence coding for dihydrodipicolinate reductase        dapB (EP 1 108 790; DNA SEQ ID No. 3477),    -   nucleotide sequence coding for diaminopicolinate-decarboxylase        lysA (EP 1 108 790 A2; DNA SEQ ID No. 3451),    -   nucleotide sequence coding for glycosyl transferase (gene bank        accession numbers NP_(—)600345 and NCgl1072) and/or    -   nucleotide sequence coding for lactate dehydrogenase (gene bank        accession number NP_(—)602107, NCgl2817).

The increase and/or decrease in the content and/or activity of theaforementioned nucleotide sequences of group I and II in comparison tothe respective wild-type or initial organism may amount to at least 10%,at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 90% or atleast 100%. Compared to such initial host organisms, the increase and/ordecrease in the content and/or activity of the aforementioned nucleotidesequences of group I and II according to the present invention canamount also preferably to at least at factor of 2, 3, 4, 5, 6, 7, 8, 9,10, 30, 50, 70, 100, 200, 500 or at least a factor of 1000.

Thus, all host cells and organisms in accordance with the presentinvention are characterized in that they comprise and preferablyover-express at least one nucleotide and preferably DNA sequence inaccordance with the present invention which encodes a protein orpolypeptide that is an enzymatically active cobalamin-dependentmethionine synthase or functional fragment thereof showing a reducedproduct inhibition in the presence of methionine as defined above. Thesepoly-peptides or proteins will usually carry at least one mutation intheir amino acid sequence in comparison with the respective wild-typeamino acid sequence which is responsible for the reduced productinhibition by methionine. In addition, these host cells may show anincrease and/or decrease in the content and/or activity of any of thenucleotide sequences as specified above for group I and group II.

Alternatively, or in addition, these host cells may show a deletion orfunctional disruption of the endogenous genes encoding for wild-typecobalamin-dependent methionine synthases. Such host cells may beselected from the organisms specified above and produced in accordancewith the methods described below.

Other embodiments of the present invention relate to methods forproducing methionine in a host cell, wherein at least one nucleotide andpreferably DNA sequence in accordance with the present invention, i.e. asequence that encodes a polypeptide or protein which is an enzymaticallyactive cobalamin-dependent methionine synthase or functional fragmentthereof with reduced product inhibition in the presence of methionine asa consequence of a mutation in the amino acid sequence, is expressed ina host organism. Such host cells may be cultivated under appropriateconditions and the produced methionine be recovered. Such methods mayalso provide an increased efficiency and/or yield of methionine incomparison to the respective starting organism.

Other embodiments of the present invention relate to the use ofnucleotide and preferably DNA sequences in accordance with the presentinvention and host cells in accordance with the present invention forproducing methionine and/or increasing the efficiency and/or yield ofmethionine production.

With respect to increasing or decreasing the amount and/or activity ofnucleotide sequences and the polypeptides being encoded thereby, allmethods that are known in the art for increasing or decreasing theamount and/or activity of nucleotide sequence and/or a polypeptide in ahost such as the above-mentioned organisms may be used. These methodsare described in further detail below. These methods may also be used toexpress a DNA sequence in accordance with the present invention, i.e. aDNA sequence encoding a cobalamin-dependent methionine synthase withreduced product inhibition in the presence of methionine as aconsequence of a mutation in the amino acid sequence.

Increasing or Introducing the Amount and/or Activity of NucleotideSequences and/or Polypeptides in Accordance with the Invention and ofGroup I

With respect to increasing the amount, two basic scenarios can bedifferentiated. In the first scenario, the amount of the polypeptide isincreased by expression of an exogenous version of the respectivenucleotide sequence. In the other scenario, expression of the endogenouspolypeptide is increased by influencing the activity of promoter and/orenhancer elements and/or other regulatory activities such asphosphorylation, sumoylation, ubiquitylation, etc. that regulate theactivities of the respective polypeptides either on a transcriptional,translational or post-translational level.

Besides simply increasing the amount of e.g. nucleotide sequencesmentioned above, the activity of the polypeptides of e.g. group I may beincreased by using enzymes carrying specific mutations that allow for anincreased activity of the enzyme. Such mutations may, e.g. inactivatethe regions of an enzyme that are responsible for feedback inhibition.By mutating these by e.g. introducing non-conservative mutations, theenzyme would not provide for feedback regulation anymore and thusactivity of the enzyme would not be down regulated if more product wasproduced. The mutations may be either introduced into the endogenouscopy of the enzyme, or may be provided by over-expressing acorresponding mutant form of the exogenous enzyme. Such mutations maycomprise point mutations, deletions or insertions. Point mutations maybe conservative or non-conservative. Furthermore, deletions may compriseonly two or three amino acids up to complete domains of the respectiveprotein. Of course, polypeptides in accordance with the invention, i.e.cobalamin-dependent methionine synthases or functional fragments thereofwith reduced product inhibition can be expressed by expression ofcorresponding exogenous nucleotide sequences or by introducing themutation(s) that leads to the reduced product inhibition in theendogenous genes.

Thus, the increase of the activity and the amount of a polypeptide maybe achieved via different routes, e.g. by switching off inhibitoryregulatory mechanisms at the transcription, translation, and proteinlevel or by increase of gene expression of a nucleic acid coding forthese proteins in comparison with the starting organism, e.g.

by manipulating the endogenous gene or by introducing nucleic acidscoding for the polypeptide.

In one embodiment, the increase of the activity and amount of apolypeptide, respectively, in comparison with the initial organism isachieved by an increase in the expression of a nucleic acid encodingsuch polypeptides. Sequences may be obtained from the respectivedatabase, e.g. at NCBI (http://www.ncbi.nlm.nih.gov/), EMBL(http://www.embl.org), or Expasy (http://www.expasy.org/).

In a further embodiment, the increase of the amount and/or activity ofthe above mentioned polypeptides is achieved by introducing thecorresponding nucleic acids into the organism, preferably C. glutamicum,E. coli, S. coel or T. maritima.

In principle, every protein of different organisms with an enzymaticactivity of the polypeptides mentioned above can be used. With genomicnucleic acid sequences of such enzymes from eukaryotic sourcescontaining introns, already processed nucleic acid sequences like thecorresponding cDNAs are to be used in the case that the host organism isnot capable or cannot be made capable of splicing the correspondingmRNAs. All nucleic acids mentioned in the description can be, e.g., anRNA, DNA or cDNA sequence.

In one method according to the present invention for producingmethionine, a nucleic acid sequence coding for one of the above-definedcobalamin-dependent methionine synthases or functional fragments thereofwith reduced product inhibition by methionine is transferred to amicroorganism such as C. glutamicum, E. coli, S. coel or T. maritima,respectively. This transfer leads to an increase in the expression ofthe mutated enzyme, and correspondingly to increased methioninesynthesis.

According to the present invention, increasing and/or introducing theamount and/or the activity of a polypeptide typically comprises thefollowing steps:

a) production of a vector comprising the following nucleic acidsequences, preferably DNA sequences, in 5′-3′-orientation:

-   -   a promoter sequence functional in the organisms of the invention    -   operatively linked thereto a DNA sequence in accordance with the        invention    -   a termination sequence functional in the organisms of the        invention

b) transfer of the vector from step a) to the organisms of the inventionsuch as C. glutamicum, E. coli, S. coel or T. maritima and, optionally,integration into the respective genomes.

The use of such vectors comprising regulatory sequences, like promoterand termination sequences are, is known to the person skilled in theart. Furthermore, the person skilled in the art knows how a vector fromstep a) can be transferred to organisms such as C. glutamicum, E. coli,S. coel or T. maritima and which properties a vector must have to beable to be integrated into their genomes.

If the enzyme content in an organism such as C. glutamicum is increasedby transferring a nucleic acid coding for a polypeptide from anotherorganism, like e.g. E. coli, it is advisable to transfer the amino acidsequence encoded by the nucleic acid sequence e.g. from E. coli byback-translation of the polypeptide sequence according to the geneticcode into a nucleic acid sequence comprising mainly those codons, whichare used more often due to the organism-specific codon usage. The codonusage can be determined by means of computer evaluations of other knowngenes of the relevant organisms.

According to the present invention, an increase of the gene expressionand of the activity, respectively, of a nucleotide sequence inaccordance with the present invention is also understood to be themanipulation of the expression of the endogenous respective endogenousenzymes of an organism, in particular of C. glutamicum, E. coli, S. coelor T. martima. This can be achieved, e.g., by altering the promoter DNAsequence for genes encoding, e.g. cobalamin-dependent methioninesynthases with reduced product inhibition. Such an alteration, whichcauses an altered, preferably increased, expression rate of thesemutated enzymes can be achieved by deletion or insertion of DNAsequences. Of course, this requires that mutations which are responsiblefor the reduced product inhibition have been introduced into theendogenous genes.

An alteration of the promoter sequence of such mutated endogenous genesusually causes an alteration of the expressed amount of the gene andtherefore also an alteration of the activity detectable in the cell orin the organism.

Furthermore, an altered and increased expression, respectively, of anendogenous gene can be achieved by a regulatory protein, which does notoccur in the transformed organism, and which interacts with the promoterof these genes. Such a regulator can be a chimeric protein consisting ofa DNA binding domain and a transcription activator domain, as e.g.described in WO 96/06166.

A further possibility for increasing the activity and the content ofendogenous genes is to up-regulate transcription factors involved in thetranscription of the endogenous genes, e.g. by means of overexpression.The measures for overexpression of transcription factors are known tothe person skilled in the art.

Furthermore, an alteration of the activity of endogenous genes can beachieved by targeted mutagenesis of the endogenous gene copies.

An alteration of endogenous genes coding for the enzymes of e.g. group Ican also be achieved by influencing the post-translational modificationsof the enzymes. This can happen e.g. by regulating the activity ofenzymes like kinases or phosphatases involved in the post-translationalmodification of the enzymes by means of corresponding measures likeoverexpression or gene silencing.

In another embodiment, polypeptides of e.g. group I may be improved inefficiency, or its allosteric control region destroyed such thatfeedback inhibition of production of the compound is prevented.Similarly, a degradative enzyme may be deleted or modified bysubstitution, deletion, or addition such that its degradative activityis lessened for the desired polypeptides or the polypeptides beingencoded by the nucleotide sequences of the present invention withoutimpairing the viability of the cell. In each case, the overall yield orrate of production of methionine may be increased.

It is also possible that such alterations in the polypeptides andnucleotide molecules may improve the production of other fine chemicalssuch as other sulfur containing compounds like cysteine or glutathione,other amino acids, vitamins, cofactors, nutraceuticals, nucleotides,nucleosides, and trehalose. Metabolism of any one compound can beintertwined with other biosynthetic and degradative pathways within thecell, and necessary cofactors, intermediates, or substrates in onepathway are likely supplied or limited by another such pathway.Therefore, by modulating the activity of polypeptides of the presentinvention and/or those of e.g. group I, the production and/or efficiencyof another fine chemical biosynthetic or degradative pathway besidesthose leading to methionine may be impacted.

Enzyme expression and function may also be regulated based on thecellular levels of a compound from a different metabolic process, andthe cellular levels of molecules necessary for basic growth, such asamino acids and nucleotides, may critically affect the viability of themicroorganism in large-scale culture. Thus, modulation of an amino acidbiosynthesis enzyme of e.g. the lysine biosynthetic pathways such thatthey are no longer responsive to feedback inhibition or such that theyare improved in efficiency or turnover may result in better methionineproduction. The aforementioned strategies for increasing or introducingthe amount and/or activity of the polypeptide and nucleotide sequencesare not meant to be limiting; variations on these strategies will bereadily apparent to one of ordinary skill in the art.

Reducing the Amount and/or Activity of Nucleotides Sequences and/orPolypeptides Encoding Endogenous Cobalamin Dependent MethionineSynthases and of Group II

For reducing the amount and/or activity of nucleotide sequence andpolypeptides being encoded thereby, various strategies are alsoavailable.

The expression of the endogenous enzymes of e.g. group II can e.g. beregulated via the expression of aptamers specifically binding to thepromoter sequences of the genes. Depending on the aptamers binding tostimulating or repressing promoter regions, the amount and thus, in thiscase, the activity of such enzymes is increased or reduced.

Aptamers can also be designed in a way as to specifically bind to theenzymes themselves and to reduce the activity of the enzymes by e.g.binding to the catalytic center of the respective enzymes. Theexpression of aptamers is usually achieved by vector-basedoverexpression (see above) and is, as well as the design and theselection of aptamers, well known to the person skilled in the art(Famulok et al., (1999) Curr Top Microbiol Immunol., 243,123-36).

Furthermore, a decrease of the amount and the activity of e.g. theendogenous genes of MetH or of the endogenous enzymes of Group II can beachieved by means of various experimental measures, which are well knownto the person skilled in the art. These measures are usually summarizedunder the term “gene silencing”. For example, the expression of anendogenous gene can be silenced by transferring an above-mentionedvector, which has a DNA sequence coding for the enzyme or parts thereofin antisense order, to the organisms such as C. glutamicum and E. coli.This is based on the fact that the transcription of such a vector in thecell leads to an RNA, which can hybridize with the mRNA transcribed bythe endogenous gene and therefore prevents its translation.

Regulatory sequences operatively linked to a nucleic acid cloned in theantisense orientation can be chosen which direct the continuousexpression of the antisense RNA molecule in a variety of cell types, forinstance viral promoters and/or enhancers, or regulatory sequences canbe chosen which direct constitutive, tissue specific or cell typespecific expression of antisense RNA. The antisense expression vectorcan be in the form of a recombinant plasmid, phagemid or attenuatedvirus in which antisense nucleic acids are produced under the control ofa high efficiency regulatory region, the activity of which can bedetermined by the cell type into which the vector is introduced. For adiscussion of the regulation of gene expression using antisense genessee Weintraub, H. etal., Antisense RNA as a molecular tool for geneticanalysis, Trends in Genetics, Vol. 1 (1) 1986.

In principle, the antisense strategy can be coupled with a ribozymemethod. Ribozymes are catalytically active RNA sequences, which, ifcoupled to the antisense sequences, cleave the target sequencescatalytically (Tanner et al., (1999) FEMS Microbiol Rev. 23 (3),257-75). This can enhance the efficiency of an antisense strategy.

Further methods are the introduction of nonsense mutations into theendogenous gene by means of introducing RNA/DNA oligonucleotides intothe organism (Zhu et al., (2000) Nat. Biotechnol. 18 (5), 555-558) orgenerating knockout mutants with the aid of homologous recombination(Hohn et al., (1999) Proc. Natl. Acad. Sci. USA. 96, 8321-8323.).

To create a homologous recombinant microorganism, a vector is preparedwhich contains at least a portion of gene coding for e.g. an enzyme ofgroup II or the endogenous MetH gene into which a deletion, addition orsubstitution has been introduced to thereby alter, e.g., functionallydisrupt, the endogenous gene.

Preferably, this endogenous gene is a C. glutamicum or E. coli gene, butit can be a homologue from a related bacterium or even from a yeast orplant source. In one embodiment, the vector is designed such that, uponhomologous recombination, the endogenous gene is functionally disrupted(i. e. no longer encodes a functional protein; also referred to as a“knock out” vector). Alternatively, the vector can be designed suchthat, upon homologous recombination, the endogenous gene is mutated orotherwise altered but still encodes functional protein (e.g., theupstream regulatory region can be altered to thereby alter theexpression of the endogenous enzyme of e.g. group 2). In the homologousrecombination vector, the altered portion of the endogenous gene isflanked at its 5′ and 3′ends by additional nucleic acid of theendogenous gene to allow for homologous recombination to occur betweenthe exogenous gene carried by the vector and an endogenous gene in the(micro)organism. The additional flanking endogenous nucleic acid is ofsufficient length for successful homologous recombination with theendogenous gene. Typically, several kilobases of flanking DNA (both atthe 5′ and 3′ ends) are included in the vector (see e.g., Thomas, K. R.,and Capecchi, M. R. (1987) Cell 51: 503 for a description of homologousrecombination vectors).

The vector is introduced into a microorganism (e.g., by electroporation)and cells in which the introduced endogenous gene has homologouslyrecombined with the endogenous enzymes are selected, using art-knowntechniques.

In another embodiment, an endogenous gene in a host cell is disrupted(e.g., by homologous recombination or other genetic means known in theart) such that expression of its protein product does not occur. Inanother embodiment, an endogenous or introduced gene in a host cell hasbeen altered by one or more point mutations, deletions, or inversions,but still encodes a functional enzyme. In still another embodiment, oneor more of the regulatory regions (e.g., a promoter, repressor, orinducer) of an endogenous gene in a (micro)organism has been altered(e.g., by deletion, truncation, inversion, or point mutation) such thatthe expression of the endogenous gene is modulated. One of ordinaryskill in the art will appreciate that host cells containing more thanone of the genes coding e.g. for the enzymes of group II and proteinmodifications may be readily produced using the methods of theinvention, and are meant to be included in the present invention.

Furthermore, a gene repression (but also gene overexpression) is alsopossible by means of specific DNA-binding factors, e.g. factors of thezinc finger transcription factor type. Furthermore, factors inhibitingthe target protein itself can be introduced into a cell. Theprotein-binding factors may e.g. be the above-mentioned aptamers(Famulok et al., (1999) Curr Top Microbiol Immunol. 243, 123-36).

As further protein-binding factors, whose expression in organisms causea reduction of the amount and/or the activity of the enzymes of e.g.group II, enzyme-specific antibodies may be considered. The productionof monoclonal, polyclonal, or recombinant enzyme-specific antibodiesfollows standard protocols (Guide to Protein Purification, Meth.Enzymol. 182, pp. 663-679 (1990), M. P. Deutscher, ed.). The expressionof antibodies is also known from the literature (Fiedler et al., (1997)Immunotechnology 3, 205-216; Maynard and Georgiou (2000) Annu. Rev.Biomed. Eng. 2, 339-76).

The mentioned techniques are well known to the person skilled in theart. Therefore, he also knows which sizes the nucleic acid constructsused for e.g. antisense methods must have and which complementarity,homology or identity, the respective nucleic acid sequences must have.The terms complementarity, homology, and identity are known to theperson skilled in the art.

The term complementarity describes the capability of a nucleic acidmolecule of hybridizing with another nucleic acid molecule due tohydrogen bonds between two complementary bases. The person skilled inthe art knows that two nucleic acid molecules do not have to have acomplementarity of 100% in order to be able to hybridize with eachother. A nucleic acid sequence, which is to hybridize with anothernucleic acid sequence, is preferred being at least 30%, at least 40%, atleast 50%, at least 60%, preferably at least 70%, particularly preferredat least 80%, also particularly preferred at least 90%, in particularpreferred at least 95% and most preferably at least 98 or 100%,respectively, complementary with said other nucleic acid sequence.

Nucleic acid molecules are identical, if they have identical nucleotidesin identical 5′-3′-order.

The hybridization of an antisense sequence with an endogenous mRNAsequence typically occurs in vivo under cellular conditions or in vitro.According to the present invention, hybridization is carried out in vivoor in vitro under conditions that are stringent enough to ensure aspecific hybridization.

Stringent in vitro hybridization conditions are known to the personskilled in the art and can be taken from the literature (see e.g.Sambrook et al., Molecular Cloning, Cold Spring Harbor Press). The term“specific hybridization” refers to the case wherein a moleculepreferentially binds to a certain nucleic acid sequence under stringentconditions, if this nucleic acid sequence is part of a complex mixtureof e.g. DNA or RNA molecules.

The term “stringent conditions” therefore refers to conditions, underwhich a nucleic acid sequence preferentially binds to a target sequence,but not, or at least to a significantly reduced extent, to othersequences.

Stringent conditions are dependent on the circumstances. Longersequences specifically hybridize at higher temperatures. In general,stringent conditions are chosen in such a way that the hybridizationtemperature lies about 5° C. below the melting point (Tm) of thespecific sequence with a defined ionic strength and a defined pH value.Tm is the temperature (with a defined pH value, a defined ionic strengthand a defined nucleic acid concentration), at which 50% of themolecules, which are complementary to a target sequence, hybridize withsaid target sequence. Typically, stringent conditions comprise saltconcentrations between 0.01 and 1.0 M sodium ions (or ions of anothersalt) and a pH value between 7.0 and 8.3. The temperature is at least30° C. for short molecules (e.g. for such molecules comprising between10 and 50 nucleotides). In addition, stringent conditions can comprisethe addition of destabilizing agents like e.g. form amide. Typicalhybridization and washing buffers are of the following composition.

Pre-Hybridization Solution:

-   -   0.5% SDS    -   5×SSC    -   50 mM NaPO₄, pH 6.8    -   0.1% Na-pyrophosphate    -   5× Denhardt's reagent        Hybridization solution: Pre-hybridization solution    -   1×10⁶ cpm/ml probe (5-10 min 95° C.)

20×SSC: 3 M NaCl

-   -   0.3 M sodium citrate    -   ad pH 7 with HCl        50× Denhardt's reagent: 5 g Ficoll    -   5 g polyvinylpyrrolidone    -   5 g Bovine Serum Albumin    -   ad 500 ml A. dest.

A typical procedure for the hybridization is as follows:

Optional: wash Blot 30 min in 1×SSC/0.1% SDS at 65° C.Pre-hybridization: at least 2 h at 50-55° C.Hybridization: over night at 55-60° C.

Washing: 05 min 2×SSC/0.1% SDS

Hybridization temperature

-   -   30 min 2×SSC/0.1% SDS    -   Hybridization temperature    -   30 min 1×SSC/0.1% SDS    -   Hybridization temperature    -   45 min 0.2×SSC/ 0.1% SDS 65° C.    -   5 min 0.1×SSC room temperature

These stringent conditions also apply as far as the claims relate to DNAsequences that hybridise under stringent conditions.

The terms “sense” and “antisense” as well as “antisense orientation” areknown to the person skilled in the art. Furthermore, the person skilledin the art knows, how long nucleic acid molecules, which are to be usedfor antisense methods, must be and which homology or complementaritythey must have concerning their target sequences.

Accordingly, the person skilled in the art also knows, how long nucleicacid molecules, which are used for gene silencing methods, must be. Forantisense purposes complementarity over sequence lengths of 100nucleotides, 80 nucleotides, 60 nucleotides, 40 nucleotides and 20nucleotides may suffice. Longer nucleotide lengths will certainly alsosuffice. A combined application of the above-mentioned methods is alsoconceivable.

If, according to the present invention, DNA sequences are used, whichare operatively linked in 5′-3′-orientation to a promoter active in theorganism, vectors can, in general, be constructed, which, after thetransfer to the organism's cells, allow the overexpression of the codingsequence or cause the suppression or competition and blockage ofendogenous nucleic acid sequences and the proteins expressed there from,respectively.

The activity of a particular enzyme may also be reduced byover-expressing a non-functional mutant thereof in the organism. Thus, anon-functional mutant which is not able to catalyze the reaction inquestion, but that is able to bind e.g. the substrate or co-factor, can,by way of over-expression out-compete the endogenous enzyme andtherefore inhibit the reaction. Further methods in order to reduce theamount and/or activity of an enzyme in a host cell are well known to theperson skilled in the art.

Vectors and Host Cells

Another aspect of the invention pertains to vectors, preferablyexpression vectors, containing a nucleotide sequence in accordance withthe invention (or portions thereof) or combinations thereof. As usedherein, the term “vector” refers to a nucleic acid molecule capable oftransporting another nucleic acid to which it has been linked.

One type of vector is a “plasmid”, which refers to a circular doublestranded DNA loop into which additional DNA segments can be ligated.Another type of vector is a viral vector, wherein additional DNAsegments can be ligated into the viral genome.

Certain vectors are capable of autonomous replication in a host cellinto which they are introduced (e.g., bacterial vectors having abacterial origin of replication and episomal mammalian vectors). Othervectors are integrated into the genome of a host cell upon introductioninto the host cell, and thereby are replicated along with the hostgenome. Moreover, certain vectors are capable of directing theexpression of genes to which they are operatively linked.

Such vectors are referred to herein as “expression vectors”.

In general, expression vectors of utility in recombinant DNA techniquesare often in the form of plasmids. In the present specification,“plasmid” and “vector” can be used interchangeably as the plasmid is themost commonly used form of vector.

The recombinant expression vectors of the invention may comprise anucleic acid in accordance with the present invention and/or coding forthe enzymes of group I in a form suitable for expression of therespective nucleic acid in a host cell, which means that the recombinantexpression vectors include one or more regulatory sequences, selected onthe basis of the host cells to be used for expression, which isoperatively linked to the nucleic acid sequence to be expressed.

Within a recombinant expression vector, “operably linked” is intended tomean that the nucleotide sequence of interest is linked to theregulatory sequence (s) in a manner which allows for expression of thenucleotide sequence (e.g., in an in vitro transcription/translationsystem or in a host cell when the vector is introduced into the hostcell). The term “regulatory sequence” is intended to include promoters,repressor binding sites, activator binding sites, enhancers and otherexpression control elements (e.g., terminators, polyadenylation signals,or other elements of mRNA secondary structure). Such regulatorysequences are described, for example, in Goeddel; Gene ExpressionTechnology: Methods in Enzymology 185, Academic Press, San Diego, CA(1990). Regulatory sequences include those which direct constitutiveexpression of a nucleotide sequence in many types of host cell and thosewhich direct expression of the nucleotide sequence only in certain hostcells. Preferred regulatory sequences are, for example, promoters suchas cos-, tac-, trp-, tet-, trp-, tet-, lpp-, lac-, 1pp lac-, lacIq-,T7-, T5-, T3-, gal-, trc-, ara-, SP6-, arny, SP02, e-Pp- ore PL, whichare used preferably in bacteria. Additional regulatory sequences are,for example, promoters from yeasts and fungi, such as ADC1, MFa, AC,P-60, CYC1, GAPDH, TEF, rp28, ADH, promoters from plants suchasCaMV/355, SSU, OCS, lib4, usp, STLS1, B33, nos or ubiquitin-orphaseolin-promoters. It is also possible to use artificial promoters. Itwill be appreciated by one of ordinary skill in the art that the designof the expression vector can depend on such factors as the choice of thehost cell to be transformed, the level of expression of protein desired,etc. The expression vectors of the invention can be introduced into hostcells to thereby produce proteins or peptides, including fusion proteinsor peptides, encoded by nucleic acids in accordance with the invention.

The recombinant expression vectors of the invention can be designed forexpression of the polypeptides in accordance with the invention inprokaryotic or eukaryotic cells. For example, the genes for the enzymesof Group I can be expressed in bacterial cells such as C. glutamicum andE. coli, insect cells (using baculovirus expression vectors), yeast andother fungal cells (see Romanos, M. A. et al. (1992), Yeast 8: 423-488;van den Hondel, C. A. M. J. J. et al.(1991) in: More Gene Manipulationsin Fungi, J. W. Bennet & L. L. Lasure, eds., p. 396-428: Academic Press:San Diego; and van den Hondel, C. A. M. J. J. & Punt, P. J.(1991) in:Applied Molecular Genetics of Fungi, Peberdy, J. F. etal., eds., p.1-28, Cambridge University Press: Cambridge), algae and multicellularplant cells (see Schmidt, R. and Willmitzer, L. (1988) Plant Cell Rep.:583-586). Suitable host cells are discussed further in Goeddel, GeneExpression Technology: Methods in Enzymology 185, Academic Press, SanDiego, Calif. (1990). Alternatively, the recombinant expression vectorcan be transcribed and translated in vitro, for example using T7promoter regulatory sequences and T7 polymerase.

Expression of proteins in prokaryotes is most often carried out withvectors containing constitutive or inducible promoters directing theexpression of either fusion or non-fusion proteins.

Fusion vectors add a number of amino acids to a protein encoded therein,usually to the amino terminus of the recombinant protein but also to theC-terminus or fused within suitable regions in the proteins. Such fusionvectors typically serve three purposes: 1) to increase expression ofrecombinant protein; 2) to increase the solubility of the recombinantprotein; and 3) to aid in the purification of the recombinant protein byacting as a ligand in affinity purification. Often, in fusion expressionvectors, a proteolytic cleavage site is introduced at the junction ofthe fusion moiety and the recombinant protein to enable separation ofthe recombinant protein from the fusion moiety subsequent topurification of the fusion protein. Such enzymes, and their cognaterecognition sequences, include Factor Xa, thrombin and enterokinase.

Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc;Smith, D. B. and Johnson, K. S. (1988) Gene 67: 31-40), pMAL (NewEngland Biolabs, Beverly, Mass.) and pRIT5 (Pharmacia, Piscataway, N.J.)which fuse glutathione S-transferase (GST), maltose E binding protein,or protein A, respectively.

Examples of suitable inducible non-fusion E. coli expression vectorsinclude pTrc (Amann et al., (1988) Gene 69: 301-315), pLG338, pACYC184,pBR322,pUC18, pUC19, pKC30, pRep4,pHS1, pHS2, pPLc236, pMBL24, pLG200,pUR290,pIN-III113-B1, egt11, pBdC1, and pET 11d (Studier etal., GeneExpression Technology: Methods in Enzymology 185, Academic Press, SanDiego, Calif. (1990) 60-89; and Pouwels etal., eds. (1985) CloningVectors. Elsevier: New York IBSN 0 444 904018). Target gene expressionfrom thepTrc vector relies on host RNA polymerase transcription from ahybrid trp-lac fusion promoter. Target gene expression from the pET 11dvector relies on transcription from a T7 gn1O-lac fusion promotermediated by a coexpressed viral RNA polymerase (T7gn1). This viralpolymerase is supplied by host strains BL21 (DE3) or HMS 174 (DE3) froma resident X prophage harboring a T7gn1 gene under the transcriptionalcontrol of the lacUV 5 promoter. For transformation of other varietiesof bacteria, appropriate vectors may be selected. For example, theplasmidsplJ101, pIJ364, pIJ702 and pIJ361 are known to be useful intransforming Streptomyces, while plasmidspUB110, pC194, or pBD214 aresuited for transformation of Bacillus species. Several plasmids of usein the transfer of genetic information into Corynebacterium includepHM1519,pBL1, pSA77, or pAJ667 (Pouwels etal., eds. (1985) CloningVectors. Elsevier: New York IBSN 0 444 904018).

One strategy to maximize recombinant protein expression is to expressthe protein in a host bacteria with an impaired capacity toproteolytically cleave the recombinant protein (Gottesman, S., GeneExpression Technology: Methods in Enzymology 185, Academic Press, SanDiego, Calif. (1990) 119-128). Another strategy is to alter the nucleicacid sequence of the nucleic acid to be inserted into an expressionvector so that the individual codons for each amino acid are thosepreferentially utilized in the bacterium chosen for expression, such asC. glutamicum (Wada et al. (1992) Nucleic Acids Res. 20: 2111-2118).Such alteration of nucleic acid sequences of the invention can becarried out by standard DNA synthesis techniques.

Examples of suitable C. glutamicum and E coli shuttle vectors can befound in Eikmanns et al (Gene. (1991) 102, 93-8).

In another embodiment, the protein expression vector is a yeastexpression vector. Examples of vectors for expression in yeast S.cerevisiae include pYepSec1 (Baldari, et al., (1987) Embo J. 6:229-234), 2i, pAG-1, Yep6, Yep13, pEMBLYe23, pMFa(Kurjan and Herskowitz,(1982) Cell 30: 933-943), pJRY88 (Schultz etal., (1987) Gene 54:113-123), and pYES2 (Invitrogen Corporation, San Diego, Calif.). Vectorsand methods for the construction of vectors appropriate for use in otherfungi, such as the filamentous fungi, include those detailed in: van denHondel, C. A. M. J. J. & Punt, P. J. (1991) in: Applied MolecularGenetics of Fungi, J. F. Peberdy, et al., eds., p. 1-28, CambridgeUniversity Press: Cambridge, and Pouwels et al., eds. (1985) CloningVectors. Elsevier: New York (IBSN 0 444 904018).

For the purposes of the present invention, an operative link isunderstood to be the sequential arrangement of promoter, codingsequence, terminator and, optionally, further regulatory elements insuch a way that each of the regulatory elements can fulfill itsfunction, according to its determination, when expressing the codingsequence.

For other suitable expression systems for both prokaryotic andeukaryotic cells see chapters 16 and 17 of Sambrook, J. et al. MolecularCloning: A Laboratory Manual. 3rd ed., Cold Spring Harbor Laboratory,Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2003.

Another aspect of the invention pertains to organisms or host cells intowhich a recombinant expression vector of the invention has beenintroduced. The terms “host cell” and “recombinant host cell” are usedinterchangeably herein. It is understood that such terms refer not onlyto the particular subject cell but also to the progeny or potentialprogeny of such a cell. Because certain modifications may occur insucceeding generations due to either mutation or environmentalinfluences, such progeny may not, in fact, be identical to the parentcell, but are still included within the scope of the term as usedherein.

Vector DNA can be introduced into prokaryotic or eukaryotic cells viaconventional transformation or transfection techniques. As used herein,the terms “transformation” and “transfection”, “conjugation” and“transduction” are intended to refer to a variety of art-recognizedtechniques for introducing foreign nucleic acid (e. g., linear DNA orRNA (e. g., a linearized vector or a gene construct alone without avector) or nucleic acid in the form of a vector (e.g., a plasmid, phage,phasmid, phagemid, transposon or other DNA) into a host cell, includingcalcium phosphate or calcium chloride co-precipitation,DEAE-dextran-mediated transfection, lipofection, natural competence,chemical-mediated transfer, or electroporation. Suitable methods fortransforming or transfecting host cells can be found in Sambrook, et al.(Molecular Cloning : A Laboratory Manual. 3rd ed., Cold Spring HarborLaboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor,N.Y., 2003), and other laboratory manuals.

In order to identify and select these integrants, a gene that encodes aselectable marker (e.g., resistance to antibiotics) is generallyintroduced into the host cells along with the gene of interest.Preferred selectable markers include those which confer resistance todrugs, such as G418, hygromycin and methotrexate. Nucleic acid encodinga selectable marker can be introduced into a host cell on the samevector as that encoding polypeptides of the present invention or can beintroduced on a separate vector. Cells stably transfected with theintroduced nucleic acid can be identified by drug selection (e. g.,cells that have incorporated the selectable marker gene will survive,while the other cells die).

In another embodiment, recombinant microorganisms can be produced whichcontain selected systems which allow for regulated expression of theintroduced gene. For example, inclusion of a nucleotide sequence of thepresent invention on a vector placing it under control of the lac operonpermits expression of the gene only in the presence of IPTG. Suchregulatory systems are well known in the art.

In one embodiment, the method comprises culturing the organisms ofinvention (into which a recombinant expression vector encoding e.g. apolypeptide of the present invention has been introduced, or into whichgenome has been introduced a gene encoding a wild-type or alteredenzyme) in a suitable medium for methionine production. In anotherembodiment, the method further comprises isolating methionine from themedium or the host cell.

Growth of Escherichia coli and Corynebacterium glutamicum-Media andCulture Conditions

The person skilled in the art is familiar with the cultivation of commonmicroorganisms such as C.glutamicum and E.coli. Thus, a general teachingwill be given below as to the cultivation of C.glutamicum. Correspondinginformation may be retrieved from standard textbooks for cultivation ofE.coli.

E. coli strains are routinely grown in MB and LB broth, respectively(Follettie, M. T., Peoples, O., Agoropoulou, C., and Sinskey, A J.(1993) J. Bacteriol. 175, 4096-4103). Minimal media for E. coli is M9and modified MCGC (Yoshihama, M., Higashiro, K., Rao, E. A., Akedo, M.,Shanabruch, W G., Follettie, M. T., Walker, G. C., and Sinskey, A. J.(1985) J. Bacteriol. 162,591-507), respectively. Glucose may be added ata final concentration of 1%. Antibiotics may be added in the followingamounts (micrograms per millilitre): ampicillin, 50; kanamycin, 25;nalidixic acid, 25. Amino acids, vitamins, and other supplements may beadded in the following amounts: methionine, 9.3 mM; arginine, 9.3 mM;histidine, 9.3 mM; thiamine, 0.05 mM. E. coli cells are routinely grownat 37 C, respectively.

Genetically modified Corynebacteria are typically cultured in syntheticor natural growth media. A number of different growth media forCorynebacteria are both well-known and readily available (Lieb et al.(1989) Appl. Microbiol. Biotechnol., 32: 205-210; von der Osten et al.(1998) Biotechnology Letters, 11: 11-16; Patent DE 4,120,867;Liebl(1992) “The Genus Corynebacterium, in: The Procaryotes, Volume II,Balows, A. et al., eds. Springer-Verlag).

These media consist of one or more carbon sources, nitrogen sources,inorganic salts, vitamins and trace elements. Preferred carbon sourcesare sugars, such as mono-, di-, or polysaccharides. For example,glucose, fructose, mannose, galactose, ribose, sorbose, ribose, lactose,maltose, sucrose, raffinose, starch or cellulose serve as very goodcarbon sources.

It is also possible to supply sugar to the media via complex compoundssuch as molasses or other by-products from sugar refinement. It can alsobe advantageous to supply mixtures of different carbon sources. Otherpossible carbon sources are alcohols and organic acids, such asmethanol, ethanol, acetic acid or lactic acid. Nitrogen sources areusually organic or inorganic nitrogen compounds, or materials whichcontain these compounds. Exemplary nitrogen sources include ammonia gasor ammonia salts, such as NH₄Cl or(NH₄)₂SO₄, NH₄OH, nitrates, urea,amino acids or complex nitrogen sources like corn steep liquor, soy beanflour, soy bean protein, yeast extract, meat extract and others.

The overproduction of methionine is possible using different sulfursources. Sulfates, thiosulfates, sulfites and also more reduced sulfursources like H₂S and sulfides and derivatives can be used. Also organicsulfur sources like methyl mercaptan, thioglycolates, thiocyanates, andthiourea, sulfur containing amino acids like cysteine and other sulfurcontaining compounds can be used to achieve efficient methionineproduction. Formate may also be possible as a supplement as are other Clsources such as methanol or formaldehyde. Particularly suited aremethanethiol and its dimer dimethyldisulfide.

Inorganic salt compounds which may be included in the media include thechloride-, phosphorous-or sulfate-salts of calcium, magnesium, sodium,cobalt, molybdenum, potassium, manganese, zinc, copper and iron.Chelating compounds can be added to the medium to keep the metal ions insolution. Particularly useful chelating compounds includedihydroxyphenols, like catechol or protocatechuate, or organic acids,such as citric acid. It is typical for the media to also contain othergrowth factors, such as vitamins or growth promoters, examples of whichinclude biotin, riboflavin, thiamine, folic acid, nicotinic acid,pantothenate and pyridoxine. Growth factors and salts frequentlyoriginate from complex media components such as yeast extract, molasses,corn steep liquor and others. The exact composition of the mediacompounds depends strongly on the immediate experiment and isindividually decided for each specific case. Information about mediaoptimization is available in the textbook “Applied Microbiol.Physiology, A Practical Approach (Eds. P. M. Rhodes, P. F. Stanbury, IRLPress (1997) pp. 53-73, ISBN 0 19 963577 3). It is also possible toselect growth media from commercial suppliers, like standard 1 (Merck)or BHI (grain heart infusion, DIFCO) or others.

All medium components should be sterilized, either by heat (20 minutesat 1.5 bar and 121 C) or by sterile filtration. The components caneither be sterilized together or, if necessary, separately.

All media components may be present at the beginning of growth, or theycan optionally be added continuously or batch wise. Culture conditionsare defined separately for each experiment.

The temperature should be in a range betweenl5° C. and 45° C. Thetemperature can be kept constant or can be altered during theexperiment. The pH of the medium may be in the range of 5 to 8.5,preferably around 7.0, and can be maintained by the addition of buffersto the media. An exemplary buffer for this purpose is a potassiumphosphate buffer. Synthetic buffers such as MOPS, HEPES, ACES and otherscan alternatively or simultaneously be used. It is also possible tomaintain a constant culture pH through the addition of NaOH or NH₄OHduring growth. If complex medium components such as yeast extract areutilized, the necessity for additional buffers may be reduced, due tothe fact that many complex compounds have high buffer capacities. If afermentor is utilized for culturing the microorganisms, the pH can alsobe controlled using gaseous ammonia.

The incubation time is usually in a range from several hours to severaldays. This time is selected in order to permit the maximal amount ofproduct to accumulate in the broth. The disclosed growth experiments canbe carried out in a variety of vessels, such as microtiter plates, glasstubes, glass flasks or glass or metal fermentors of different sizes. Forscreening a large number of clones, the microorganisms should becultured in microtiter plates, glass tubes or shake flasks, either withor without baffles. Preferably 100 ml shake flasks are used, filled with10% (by volume) of the required growth medium. The flasks should beshaken on a rotary shaker (amplitude 25 mm) using a speed-range of100-300′rpm. Evaporation losses can be diminished by the maintenance ofa humid atmosphere; alternatively, a mathematical correction forevaporation losses should be performed.

If genetically modified clones are tested, an unmodified control cloneor a control clone containing the basic plasmid without any insertshould also be tested. The medium is inoculated to an OD600 of 0.5-1.5using cells grown on agar plates, such as CM plates (10 g/l glucose, 2,5g/l NaCl, 2 g/l urea, 10 g/l polypeptone, 5 g/l yeast extract, 5 g/lmeat extract, 22 g/l NaCl, 2 g/l urea, 10 g/l polypeptone, 5 g/l yeastextract, 5 g/l meat extract, 22 g/l agar, pH 6.8 with 2M NaOH) that hadbeen incubated at 30 C.

Inoculation of the media is accomplished by either introduction of asaline suspension of C. glutamicum cells from CM plates or addition of aliquid preculture of this bacterium.

The above culture and media conditions may also be applied for otherhost organisms such as S. coel and T. maritima.

1-27. (canceled)
 28. An isolated polynucleotide which encodes apolypeptide comprising SEQ ID NO:2 with a mutation at position 86wherein the polypeptide exhibits cobalamin-dependent methionine synthaseactivity.
 29. The isolated polynucleotide of claim 28, wherein thepolypeptide is SEQ ID NO:1 with a mutation at position
 86. 30. Theisolated polynucleotide of claim 28, wherein the polypeptide has amutation in its homocysteine-binding domain.
 31. The isolatedpolynucleotide of claim 28, wherein the polypeptide exhibits reducedproduct inhibition by methionine.
 32. The isolated polynucleotide ofclaim 28, wherein the mutation is Phenylalanine at position 86 isreplaced by Leucine.
 33. The isolated polynucleotide of claim 28,wherein the polypeptide is selected from the group consisting of: SEQ IDNO: 19, SEQ ID NO: 20, SEQ ID NO: 21, and SEQ ID NO:
 22. 34. Anexpression vector comprising the polynucleotide of claim
 28. 35. A hostcell which comprises the polynucleotide of claim
 28. 36. The host cellof claim 35, wherein the host cell is a microorganism selected from thegroup consisting of: Corynebacterium glutamicum, Escherichia coli,Streptomyces coelicolor and Thermotoga maritima.
 37. The host cell ofclaim 35, wherein one or more of the endogenous genes of the host cellwhich encode cobalamin-dependent methionine synthetase is deleted orfunctionally disrupted.
 38. The host cell of claim 35, wherein theamount and/or activity of at least one of the following nucleotidesequences selected from the group consisting of: nucleotide sequencecoding for aspartate kinase lysC, nucleotide sequence coding forglycerine aldehyde-3-phosphate dehydrogenase gap, nucleotide sequencecoding for 3-phosphoglycerate kinase pgk, nucleotide sequence coding forpyruvatecarboxylase pyc, nucleotide sequence coding for triosephosphateisomerase tpi, nucleotide sequence coding forhomoserin-O-acetyltransferase metA, nucleotide sequence coding forcystathione-gamma-synthase metB, nucleotide sequence coding forcystathione-gamma-lyase metC, nucleotide sequence coding forserin-hydroxymethyl transferase glyA, nucleotide sequence coding forO-acetylhomoserine-sulfhydrylase metY, nucleotide sequence coding forphosphoserine aminotransferase serC, nucleotide sequence coding forphosphoserine-phosphatase serB, nucleotide sequence coding for serineacetyltransferase cysE, nucleotide sequence coding forhomoserine-dehydrogenase horn, nucleotide sequence coding for methioninesynthase metE, nucleotide sequence coding forphosphoadenosine-phosphosulfate-reductase cysH, nucleotide sequencecoding for sulfate adenylyl transferase-subunit I, nucleotide sequencecoding for CysN-sulfate adenylyl transferase-subunit 2, nucleotidesequence coding for ferredoxin-NADP-reductase, nucleotide sequencecoding for ferredoxin, nucleotide sequence coding forglucose-6-phosphate-dehydrogenase, and nucleotide sequence coding forfructose-1-6-bisphosphatase is increased in comparison to thecorresponding parent strain.
 39. The host cell of claim 35, wherein theamount and/or activity of at least one of the following nucleotidesequences selected from the group consisting of nucleotide sequencecoding for homoserine kinase thrB, nucleotide sequence coding forthreonine dehydratase ilvA, nucleotide sequence coding for threoninesynthase thrC, nucleotide sequence coding formeso-diaminopimelate-D-dehydrogenase ddh, nucleotide sequence coding forphosphoenolpyruvate carboxy kinase pck, nucleotide sequence coding forglucose-6-phosphate-6-isomerase pgi, nucleotide sequence coding forpyruvate-oxidase poxB, nucleotide sequence coding fordihydrodipicolinate synthase dapA, nucleotide sequence coding frodihydrodipicolinate reductase dapB, nucleotide sequence coding fordiaminopicolinate-decarboxylase lysA, nucleotide sequence coding forglycosyl transferase and nucleotide sequence coding for lactatehydrogenase is reduced in comparison to the corresponding parent strain.40. A method of producing methionine which comprises a) cultivating thehost cell of claim 35, and b) isolating the methionine.
 41. A method ofproducing methionine which comprising: a) transfecting the vector ofclaim 35 into a host cell, b) culturing the host cell, and c) optionallyrecovering the methionine